Sigmar Gabriel, the German Foreign Minister, criticised Trump's "short-sighted" policies that have "weakened the West" and hurt European interests.
Gabriel said that "anyone who accelerates climate change by weakening environmental protection, who sells more weapons in conflict zones and who does not want to politically resolve religious conflicts is putting peace in Europe at risk".
"The short-sighted policies of the American Government stand against the interests of the European Union," he said, judging that "the West has become smaller, at least it has become weaker".
Trump has said he will make his "final decision" this week on whether to withdraw the US from the 2015 Paris climate accord.
Steffen Seibert, Merkel's spokesman, said the Chancellor was "a convinced transatlanticist" and US-German relations "are a strong pillar of our foreign and security policy. Precisely because they are so important, it's right to name differences honestly."
Germany is bracing for national elections in September.
British Prime Minister Theresa May said she wanted to maintain a strong partnership with the European Union over security and trade after Merkel's suggestion that the continent could no longer completely rely on Britain.
May said it was right for the rest of the bloc to look at its future but made it clear that Britain wanted to remain a key partner.
"We are not leaving Europe. We are leaving the European Union," she told a campaign event in London.
"We continue to want a deep and special partnership with the remaining 27 countries in the European Union and we will continue to be committed to working with others in Europe both in terms of ... a comprehensive free trade agreement but also in terms of our security," she said.
The Paris agreement calls for "holding the increase in the global average temperature this century to well below 2C above pre-industrial levels".
It has been signed by nearly 200 countries and was considered by US President Barack Obama to be a major part of his legacy.
Trump repeatedly expressed scepticism about climate change on the campaign trail last year, although later said he had an "open mind" on the issue.