At a news conference with German Finance Minister Wolfgang Schaeuble, Mr Mnuchin said that President Donald Trump views trade as important for economic growth.
But when asked whether the Group of 20 finance ministers should explicitly reaffirm their past vow to resist protectionism, Mr Mnuchin repeated his view that some U.S. trade relationships need to be re-examined to make them fairer and more reciprocal.
"It is not our desire to get into trade wars," Mr Mnuchin said. "The president does believe in free trade but he wants free and fair trade."
Differences over trade could become a sticking point for G20 finance officials at a meeting in the spa town of Baden-Baden, Germany this weekend.
Mr Schaeuble told Reuters in an interview that it was unclear whether the anti-protectionism language would remain in the G20 statement to be issued at the meeting's close on Saturday.
Given that Mr Trump's "America First" agenda, trade issues could be set aside for G20 leaders to tackle at a summit in July, Mr Schaeuble said.
But both Mr Schaeuble and Mr Mnuchin both said they had a constructive discussion ahead of the G20 meeting and pledged to work together through differences to promote growth.
"It was a good start," Mr Schaeuble said of the meeting, adding that it was a positive sign for international cooperation and the G20 process.
"We have found a good basis to talk openly about issues where we don't have the same stance from the outset," Mr Schaeuble said.
Mr Mnuchin said the ministers agreed that they should fight currency manipulation.
The US Treasury chief declined to comment specifically on the euro's current value, but in a shift away from criticism by White House National Trade Council Director Peter Navarro that Germany has benefited unfairly from the euro's weakness, Mr Mnuchin acknowledged that the euro is used by many countries and is affected by many factors.
"It is different than a single currency controlled by a single country," Mr Mnuchin said of the euro. He also said that for trade, he views the European Union as both a single bloc as well as individual countries.
Regarding the US dollar, Mr Mnuchin reiterated his view that a strengthening dollar was good for the long run, but declined to comment on short term movements in the dollar. In recent weeks, he has said that short-term dollar spikes can be negative for the US economy.
"I believe that in the long-term best interests, the strengthening of the dollar is a good thing and I think that the long term strengthening of the dollar is a sign of confidence in the reserve currency," he said.