In interviews with German media Sunday, Adil Yigit said he had been told to leave the country by January or face deportation, adding that he feared persecution in Turkey if he returned.
“Mr Yigit has received no notice of expulsion and there are no plans to deport him,” the Hamburg immigration authority told public broadcaster ARD.
While officials had not renewed a temporary residency permit, they had in the same letter written to him that he would receive a different form of leave to stay, they said.
“The responsible immigration office agreed this procedure with Mr Yigit and his lawyer in advance,” they added.
The journalist, who says he has lived in Germany for 36 years, wore a T-shirt emblazoned with the words “freedom for journalists in Turkey” at a Berlin press conference by Merkel and Erdogan in September.
He was escorted from the chancellor's office by security guards as the Turkish president – who has locked up thousands of academics, journalists and other supposed opponents since a 2016 coup attempt – looked on.
“At chancellery press conferences, we do things the same way as in the Bundestag (parliament): no demonstrations or declarations of political causes,” Merkel's spokesman Steffen Seibert later tweeted after widespread public criticism.
The left-leaning Taz newspaper, where Yigit is a columnist, first reported about the supposed expulsion, stating that the reasons given by the authorities for Yigit's deportation are that he is not gainfully employed and does not live with his children.
Yigit also publishes a Turkish-language online newspaper, Aurupa Postasi, which is critical of Erdogan's government.