WASHINGTON — For the first time in the history of the modern Turkish republic, Turkey’s military has boycotted swearing-in ceremonies for the country’s new president, a sign of rising tensions between the largely secular military and Turkey’s Islamist ruling party.

Abdullah Gul was sworn in as Turkey’s president yesterday, making him the commander in chief of a powerful military whose generals have protested the concentration of power for his Justice and Development Party, or AKP. At the center of the controversy is Mr. Gul himself. A devout Muslim, Mr. Gul’s wife wears a traditional “turban” head covering, a political statement in a country that bans the Islamic hijab for women in government offices and schools. His political rivals have said the former foreign minister and prime minister is a stalking horse for radical Islam and that Mr. Gul eventually seeks to return Turkey to Islamic rule.

Mr. Gul did not bring his wife to yesterday’s ceremony and, in a speech to Parliament after taking the oath of office, affirmed that “Turkey is a secular democracy … these are basic values of our republic and I will defend and strengthen these values.”

In an interview from Istanbul yesterday, a former Turkish parliamentarian with the secularist Youth Party, Emin Sirin, told The New York Sun that he was not concerned that Mr. Gul would break the country’s strong ties with America, Israel, or NATO.

“I am concerned that he will bring slowly an Islamic fascism here,” he said. “The AKP are very clever people; they will not adopt the attitudes of Hamas or the Iranian clergy at first. What they are going to do, with the majority they have and the support of the population, is show that they can govern for 10 to 15 years. They will educate a new generation and slowly turn Turkey into the Malaysia model, where people have the choice to follow the secular or Islamic law.”

On Monday, Turkey’s top military leader, General Yasar Buyukanit, warned that the new ruling party could be trying to undermine the secular republic created by Mustafa Kemal Ataturk on October 29, 1923. Two years later, the first president of modern Turkey abolished the Muslim caliphate that had ruled the Ottoman Empire. Islamists in the Middle East today have stated that they seek to restore Turkey to the Islamic rule that Ataturk destroyed.

Mr. Sirin told the Sun that he fears his experience since retiring from Parliament last month may be a harbinger of things to come in Turkey under the Islamists: On August 18, he was held by the national counterterrorism police for 36 hours based on anonymous allegations that he said were trumped up to punish him for his political activities.

“They searched my house without me being present, they took up my computer. They came to the Youth Party, they searched my office in the party, they took my computers, they searched the hard drives with no warrant from the judge,” he said.

The arrest and search, according to Mr. Sirin, was the first time a former member of Parliament has been targeted by the national police in Turkey since the 1983 elections that ended a military regime that had begun in 1980.

Mr. Sirin said he has sent a letter to Mr. Erdogan to protest the investigation and to demand the evidence used to justify the search of his home and offices.

In addition to his own detention, he said many Turkish journalists with a history of expressing skepticism about the AKP’s commitment to secular rule have been asked by government officials to tone down their criticism — requests that amount to veiled threats, he said.

“When I talk to my friends in the media, there is tremendous pressure on them. The moment they publicize anything against the AKP, immediately they receive a telephone call from the AKP saying, ‘You should not criticize us,'” Mr. Sirin said.

American diplomats have been meeting with members of Turkey’s Islamist parties since the end of the Cold War, and the State Department has pointed to the AKP as a model for Islamists to participate in open democratic political systems.

Yesterday, President Bush congratulated Mr. Gul in a telephone call. A State Department deputy spokesman, Tom Casey, hailed Mr. Gul’s election as a “testament to the maturity of Turkish democracy and the strength of the Turkish constitution.”