Binali Yildirim says Turkey probing some people in US mission for links to FETO.
In the ruling Justice and Development (AK) Party's parliamentary group meeting, Yildirim said: "The U.S. took a decision which did not comply with the alliance."
Yildirim said that the two countries should solve issues between them through talks.
He stressed: "The [visa] issue should be solved as soon as possible."
The U.S. on Sunday suspended non-immigrant visa operations at all diplomatic facilities in Turkey, saying it was reassessing Turkey's commitment to the security of U.S. facilities and personnel.
Turkey retaliated by suspending non-immigrant visa service in the U.S. citing security concerns.
Yildirim said security concerns were not the real reasons behind the decision to suspend the visa service.
Links to FETO
“We are probing some people working in the American mission for possible links to FETO,” he said, adding that no one was above the law in Turkey, even if they worked in U.S. missions.
He added: “Have you asked us before jailing a deputy director general at one of our official banks when on duty in your country?”
Mehmet Hakan Atilla, deputy general manager of Turkey’s Halkbank, was arrested in the U.S. for alleged violation of U.S. sanctions against Iran.
"Why are you still harbouring the head of the July 15 coup attempt?” he said.
Fetullah Terrorist Organization (FETO) and its U.S.-based leader Fetullah Gulen orchestrated the attempted coup, which left 250 people martyred and nearly 2,200 injured.
Last week, Turkish national Metin Topuz, confirmed by the U.S.’ Istanbul Consulate as a local employee, was remanded in custody over terror charges by an Istanbul court.
Topuz is suspected to be linked to FETO.
Support to PKK
Yildirim called on the U.S. administration to deal with last year's defeated coup attempt and its aftermath. "Why don't over 80 percent of Turkish people sympathize with the U.S.? The U.S should find answer to this question."
Yildirim said the U.S. should immediately stop supporting PKK-linked PYD and YPG terrorist organizations. "Working with our enemies is not what allies do."
"Allies work together in both good and bad times," said Yildirim, adding that U.S. support to the terrorist PKK/PYD could not be accepted.
Turkey, along with the U.S. and EU, considers the PKK -- of which the PYD is an offshoot -- a terrorist organization.
Following a years-long hiatus, the PKK resumed its armed campaign against Turkey in 2015. Since then, it has been responsible for the deaths of some 1,200 Turkish security personnel and civilians, including women and children.
The U.S. has continued to support the PYD, PKK’s affiliate in Syria.