A spokesman for Merkel said she believes the travel ban is wrong.
Germany's DPA news agency quoted Merkel's spokesman Steffen Seibert as saying: "She is convinced that even the necessary, resolute fight against terrorism doesn't justify putting people of a particular origin or particular faith under general suspicion".
Merkel and Trump spoke by phone on Saturday for the first time since his inauguration.
The German Chancellor has welcomed more than a million refugees into the country, many fleeing war torn Syria.
The policy has been praised by many but also caused significant internal political difficulties, with right-wing populist parties such as Alternative for Germany (AfD) gaining ground in the last year.
Source: The Independent