Bavarian Governor and Chairman of the Bavarian Christian Democrats (CSU) Horst Seehofer (L) and Angela Merkel German Chancellor speak during a press conference after the annual meeting of the CSU at Wildbad-Kreuth on January 6, 2015 in Kreuth, Germany.

A prominent ally of Germany's Angela Merkel has threatened to take her government to court over its open door refugee policy as political pressure grows for the chancellor to reduce the number of new arrivals.

Bavarian state premier Horst Seehofer said he would send the federal government a written request within the next two weeks to restore "orderly conditions" at the nation's borders, through which one million migrants and refugees passed last year alone.

"If it doesn't follow, the state government will have no other choice but to file a suit at the Federal Constitutional Court," Seehofer told Der Spiegel magazine on Saturday.

Seehofer has issued a series of ultimatums to Merkel in recent months to press her into taking immediate action to limit the influx of migrants, only to back down at the last minute.

His comments reflect growing doubt among Germans about Merkel's "we can do this" mantra in the face of Europe's biggest migrant crisis since World War Two, especially since sexual assaults in Cologne on New Year's Eve were blamed on migrants.

Merkel's popularity has dropped since the assaults, a poll showed on Friday.

Bavaria, a conservative state that borders Austria to the south, is the home of Seehofer's Christian Social Union (CSU), sister party to Merkel's Christian Democratic Union (CDU), and is the main entry point for migrants and refugees.

The state's finance minister, Markus Soeder, told Der Spiegel that Merkel's refugee policy was not democratically legitimized and said parliament should vote on the matter.

Senior figures from the Social Democrats (SPD), Merkel's second coalition partner, have also broken ranks in recent days.