Free Exercise Clause. Free Exercise Clause refers to the section of the First Amendment italicized here: Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof… Historically, the Supreme Court has been inconsistent in dealing with this problem.The executive order President Trump is expected to sign Thursday will be focused on the Johnson Amendment and allow non-profit organizations to deny certain health coverage for religious reasons, administration sources told Fox News Wednesday.

The three main points of the executive order, according to a senior White House official, will declare “that it is the policy of the administration to protect and vigorously promote religious liberty,” direct the IRS “to exercise maxim enforcement of discretion to alleviate the burden of the Johnson Amendment,” and provide “regulatory relief for religious objectors to Obamacare’s burdensome preventive services mandate.”

The timing and contents of the order, which would come on the National Day of Prayer, are still “very fluid” and there are still several drafts, according to a senior administration official.

The Johnson Amendment, named for then-Senator Lyndon B. Johnson of Texas and enacted into law in 1954, essentially regulates tax-exempt organizations such as churches, and religious groups from being too politically involved.

Trump previously campaigned against the amendment, and in February said he would “destroy” the amendment that conservative groups claim restricted political speech by tax-exempt churches.

“I think how the president feels about Johnson amendment is that politicians and unelected bureaucrats shouldn’t have the power to shut up their critics just because they are church leaders or charities,” a senior White House official told Fox News.

In addition, sources tell Fox News the executive order will also allow non-profit organizations, hospitals, educational institutions, and businesses to deny certain health coverage for religious reasons,. That would entail protecting Christian groups like Little Sisters of the Poor from being forced to pay for abortion services.

An early draft of the order, leaked in February, would have established broad exemptions for people and groups to claim religious objections under strong language. Vice President Pence has been a proponent of the plan, and his office has been reportedly pushing for it for months.

While governor of Indiana, Pence signed a similar state law on religious liberty that stirred up controversy across the country, but was seen as a legislative win and rallying cry for social conservatives.

Progressive critics have argued the executive order would allow discrimination against the LGBT community at the federal level.

“The ACLU fights every day to defend religious freedom, but religious freedom does not mean the right to discriminate against or harm others,” Louise Melling, deputy legal director of the American Civil Liberties Union said in a statement Wednesday. “If President Trump signs an executive order that attempts to provide a license to discriminate against women or LGBT people, we will see him in court.”

A senior White House official however pushed back on the criticism saying the order “is not about discrimination.”

‘We don’t have any plans to discriminate, we’re about not discriminating against religious organizations,” the official said.

“Everything that is legal stays legal, everything that is illegal stays illegal,” the official added.

Fox News’ John Roberts and Serafin Gomez contributed to this report.

By JOE COCHRANEDEC. 13, 2016

JAKARTA, Indonesia — The Christian governor of Jakarta, the capital of Indonesia, the world’s most populous Muslim-majority nation, tearfully denied on Tuesday that he had intended to insult Islam as his trial on blasphemy charges began.

Some analysts have said the trial is a plot to keep the governor, Basuki Tjahaja Purnama, from being elected to the office, which he inherited when his predecessor won the presidency in 2014. Others say that his comments are being exploited in an effort to incite ethnic and religious hatred against Mr. Basuki, who is ethnic Chinese and the first Christian in nearly 50 years to govern Jakarta.

Mr. Basuki, known as Ahok, is charged with violating blasphemy laws during a speech to fishermen in September.

In that address, Mr. Basuki lightheartedly cited a verse of the Quran that warns Muslims against taking Christians and Jews as allies. He said at the time that given Indonesia’s transition to democracy in 1999, it was perfectly acceptable for Muslim voters to choose a Christian in the election for governor in February.

The remark was directed at “unscrupulous politicians who don’t want to compete fairly in the election,” Mr. Basuki, 50, told the three judges at the trial. If found guilty, he faces up to five years in jail.

After decades of authoritarian rule, Indonesia has come to be seen as a relatively stable, tolerant democracy. Suharto, the army leader who became president and ruled Indonesia for 32 years after seizing power in the late 1960s, signed a decree about three decades ago banning provocative political discourse on ethnicity, race and religion in an effort to maintain public order, and racial and religious harmony.

The practice of avoiding those sensitive topics appears to have been broken in the pending election for the governorship of Jakarta, the most powerful provincial post in the country and one that President Joko Widodo, a longtime ally of Mr. Basuki’s, used as a springboard to the presidency.

“The manipulation of race and religion, such as the blasphemy charge against Ahok, in a political campaign to crush an opponent, breaks the long-held taboo against using these issues brazenly to gain political advantage,” said Douglas Ramage, a political analyst based in Jakarta.

The United States and other Western nations have long held up Indonesia, which has more than 190 million Muslims but also influential Christian, Hindu and Buddhist minorities, as a model for religious pluralism and democracy in the region. The case may threaten that reputation.

“Economics, religion, ethnicity and wealth inequality are all mixed in Indonesia in a volatile way. So a moment like this, the Ahok trial, is potentially explosive,” said Jeffrey A. Winters, a professor of politics at Northwestern University who is a longtime observer of Indonesian affairs.

Supporters of Mr. Basuki, as well as many independent analysts, have said that opposition parties fielding candidates in the coming election have used the governor’s comments to elicit ethnic and religious hatred against him.

“In Indonesia’s democratic reform era, people like Ahok are being added” to the political elite, said Yenny Wahid, co-chairwoman of the Indonesia-U.S. Council on Religion and Pluralism, an independent advocacy group.

“But some people are saying, ‘Chinese dominate the economic sphere in Indonesia. Now you want to dominate politics?’ It creates fear,” added Ms. Wahid, the daughter of former President Abdurrahman Wahid, a revered Islamic cleric who fought for religious pluralism in Indonesia.

Mr. Basuki has also been attacked for his Chinese ancestry on social media in recent months.

Common slurs leveled against Mr. Basuki have suggested that he “hates Islam” and should “go back to China.” Mr. Joko, whose governing party supports Mr. Basuki’s bid for the governorship, has also been the subject of attacks.

Islamist groups, including organizations that have long demanded that the secular government be replaced by an Islamic state, have continually protested Mr. Basuki’s tenure. They have appealed to Muslim residents in the city not to vote for him. If he wins, he would be the first ethnic Chinese Christian directly elected to the office.

In recent weeks, hard-line Muslim groups have staged three mass protests in Jakarta against Mr. Basuki that drew hundreds of thousands of people — most from outside the capital — to demand that the governor be jailed for blasphemy. Some called for him to be lynched.

One march in early November ended in riots that killed one person and injured more than 200, but a protest this month that drew more than 200,000 ended peacefully.

Neither Mr. Basuki nor Mr. Joko has directly accused opposition parties of being behind the protests. But the president has said that “political actors” had taken advantage of Islamist anger to incite violence. Both opposition parties, the Great Indonesia Movement Party, also known as Gerindra, and the Democratic Party, have denied being involved in planning the protests, but they have supported the goal of jailing Mr. Basuki for blasphemy and have sought to link Mr. Joko to that controversy.

Before a large demonstration against Mr. Basuki this month, the Indonesian police arrested 11 people on charges including treason against Mr. Joko’s government.

One of Mr. Basuki’s opponents in the election is Anies Baswedan, a former minister of higher education. He is backed by Gerindra, which is led by Prabowo Subianto, a former general who lost the bitterly fought 2014 presidential election to Mr. Joko.

The other candidate is Agus Harimurti Yudhoyono of the Democratic Party, a former army officer and the son of Mr. Joko’s predecessor, Susilo Bambang Yudhoyono.

Follow Joe Cochrane on Twitter @datelinejakarta.

Muhammad Rusmadi contributed reporting.