Asked if the US would defend the Baltic states in the case of a Russian attack, Trump replied that as president he would decide on a case by case basis.
"If they fulfil their obligations to us, the answer is yes," he told the New York Times.
That position puts him potentially at odds with NATO's Article 5 commitment to collective defense which means that an attack on one member state is regarded as an attack on all.
Article 5 was invoked following the 2001, September 11 terrorist attacks on the United States and saw countries including Latvia, Estonia and Lithuania sending troops to NATO's counter-terror mission in Afghanistan.
Trump is due to expand on his foreign policy position later at the Republican National Convention that is approving his bid for the White House.
Estonian President Toomas Hendrik Ilves was first to react to Trump's words, tweeting:
We are equally committed to a l l our NATO allies, regardless of who they may be. That's what makes them allies.— toomas hendrik ilves (@IlvesToomas) July 21, 2016
Soon afterwards, Latvian President Raimonds Vejonis released a statement of his own to LSM, saying:
"The president does not want to comment on the US election campaign. At the same time, he points out that at the recent NATO summit in Warsaw, all members of the Alliance made clear their readiness to meet their obligations, including Article 5 of the NATO Treaty, which provides that in the case of a Member State facing attack, the rest are obliged to come to its aid."
The Warsaw summit's decision to deploy four new multinational battalions to the Baltic States and Poland, "clearly demonstrates NATO's determination to strengthen the defense of its eastern members," he said.
"The President also believes NATO's decision reiterates the the need for Latvia to fulfill its obligations and ensure that by 2018 defense spending comprises at least 2% of GDP," the statement added.