An American pastor detained in Turkey for nearly a year on terrorism-related charges faces new charges including espionage, in a widening case that has become a top priority in Turkey for the Trump administration.

Andrew Brunson, a Presbyterian minister who had lived and preached in Turkey for two decades before he was detained last October, faces four new charges, according to people familiar with his case and Turkish state media.

Turkey’s state-run news agency reported the new charges against Mr. Brunson late Thursday. They include “gathering state secrets for espionage, attempting to overthrow the Turkish parliament and government, and to change the constitutional order,” Anadolu Agency said. Mr. Brunson has denied the charges, the news agency reported.

The new developments came just as President Recep Tayyip Erdogan increased his control over Turkey’s main intelligence agency in a decree published early Friday. The decree further consolidates government control under the state of emergency in effect since last year’s failed coup.

Mr. Brunson was initially detained last October without charge, swept up in a broad government purge of public officials and civil society in Turkey following a summer coup attempt last year.

He was charged in December with being a member of a terrorist organization, which Turkish authorities later identified as the network of Fethullah Gülen, a Turkish cleric living in Pennsylvania.

“These are absurd charges, Andrew is not a spy,” said Ihsan Ozbek, a Turkish pastor who has known Mr. Brunson for years and who heads the Protestant Churches Foundation in Izmir, with 46 member churches across Turkey. “It’s a political case,” he said, adding that it would be unusual for a Christian pastor to find common cause with Mr. Gulen’s Islam-based movement.

“The charges that are leveled against him are absolutely false,” said Jay Sekulow, a lawyer who is representing Mr. Brunson and who is also part of President Trump’s private legal team.

Mr. Brunson’s case caught the attention of the Trump administration in its early months, with officials calling his detention wrongful. President Donald Trump raised Mr. Brunson’s case with President Erdogan on his visit to the White House in May, according to U.S. officials. Vice President Mike Pence and Secretary of State Rex Tillerson have also taken an interest in the case.

Some administration officials were hoping to secure Mr. Brunson’s release in the same way a diplomatic intervention earlier this year secured the release of an American-Egyptian aid worker imprisoned in Egypt for three years. Mr. Sekulow said American and Turkish officials have discussed the possibility of swapping Mr. Brunson in a prisoner exchange. “The increased charges are typical in these kinds of cases to up the ante, except the Turks are a NATO ally and they shouldn’t be doing this,” Mr. Sekulow said.

A Turkish official said he couldn’t comment on the case, which was a matter for the judiciary. In Washington, State Department spokeswoman Heather Nauert said Thursday State Department officials are closely tracking Mr. Brunson’s case. “Pastor Brunson has not been forgotten,” she said.

A State Department official said Friday that embassy officials last visited Mr. Brunson on Thursday and have had regular access to him.​

Mr. Brunson, who is from Black Mountain, N.C., has lived in Turkey since 1993. He was a pastor of two Protestant congregations and was involved in humanitarian efforts with refugees, according to Mr. Ozbek, the Turkish pastor. Mr. Brunson and his wife raised three children in their two decades in Turkey.

Mr. Brunson appeared before a court via video from a maximum-security prison in Izmir, the coastal city where he lived and was first detained, according to Anadolu, the Turkish news agency. The agency didn’t say when the court appearance happened.

The news agency said Mr. Brunson denied all charges and said his only aim was “to disseminate Jesus’ message.” It quoted him as saying: “I demand an explanation as to when, where and how I conducted espionage.”

The Turkish government accuses Mr. Gülen, the Turkish cleric living in Pennsylvania, of masterminding the failed coup in July last year. Mr. Gulen denies any involvement. Turkey has demanded his extradition but U.S. officials have said Turkey’s evidence isn’t strong enough.

The Gulen extradition issue was a point of tension in U.S.-Turkish relations in the last year of the Obama administration. Turkish officials have hoped for a better relationship with President Trump and worked to rebuild confidence with the new administration, especially as Ankara’s relations with European allies has soured.

On Friday, a decree issued under Turkey’s state of emergency, which has been in place since the coup attempt, authorized a process for the extradition of foreign prisoners and raised the potential of prisoner swaps.

The decree, published in the Turkish government’s official gazette, authorizes the extradition of foreign nationals imprisoned or convicted in Turkey if requested by the Turkish foreign minister and approved by the president.

The new rule also authorizes potential swaps of foreigners detained in Turkey with individuals incarcerated abroad, though it doesn’t specify the nationality of those abroad considered eligible for swaps.

Turkey has detained a number of U.S. and European nationals since the failed coup, including journalists and aid workers. And Ankara has expanded efforts to corral suspected followers and sympathizers of Mr. Gulen, the U.S.-based cleric, beyond Turkey. Authorities have sought their arrest in the U.S. and Europe, heightening tensions with Western nations who have criticized the effort.

In June, President Erdogan tried privately to secure a swap deal with Germany, offering to release a detained German-Turkish journalist in exchange for the extradition to Turkey of two Turkish generals; Germany rejected the offer. German and other European officials say the offer suggested Turkey’s leader was using the cases of foreigners detained in Turkey for political aims.

Another decree published Friday increased Mr. Erdogan’s control over Turkey’s main intelligence agency. The National Intelligence Agency, which oversees both domestic and foreign intelligence activities, will report to the country’s president instead of the prime minister. The edict also gives Mr. Erdogan oversight of new appointments at the agency, and makes him chair of a new panel to coordinate intelligence.

The steps are some of Mr. Erdogan’s most direct yet to reshape Turkey’s state institutions, using emergency powers put in place to prosecute suspected coup participants and to restore order following the upheaval in July 2016.

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