In a letter to supporters of his ministry, Rev Gottfried Martens alleged: "We have also experienced how the almost exclusively Muslim translators deliberately stick the knife in our congregational members by falsely translating what they say."
The pastor claimed that because the translators were often unfamiliar with Christian language, they were unable to properly translate a full statement from the asylum seekers.
Rev Martens wrote: "Many hearings are more like kangaroo courts in which our congregational members and candidates for baptism have absolutely no chance of presenting what is important to them. And then they must repeatedly undergo being mocked and laughed at when they relate how it is important to them that Jesus Christ died for their sins on the Cross.
"One of the hearers is known to write down in the report, when such remarks are made: "what the applicant says here makes absolutely no sense'."
Rev Martens, pastor of the Lutheran Dreieinigkeits Gemeinde, says he has baptised over 1000 former Muslims, mostly from Iran and Afghanistan.
He said that Christian converts from Islam often face rejection by their communities and even death threats.
Premier contacted Germany's Ministry for Immigration and Refugees (BAMF) over the pastor's concerns.
Spokesperson Kira Gehrmann told Premier: "The quality of translation is really important to the Federal Office. The Federal Office pursues all indications on quality of translators which reaches it. If the allegations should harden after further verification, the Federal Office refrains from using the translator in question again for the asylum procedure."
Gehrmann added that the translators are not the decision makers in the process and that asylum seekers are entitled to request another translator if they are unhappy with the one given to them.
She said that it is necessary to find out more about the asylum seekers' beliefs because religion can be used as a "tactic" in order to stay in Germany.
Gehrmann said that the line of questioning was not an "examination on belief" but "more about the person themselves. Why did they change his/ or her belief, how could they exercised their faith until now, what do they like about their new religion."