The US State Department on Wednesday also slapped sanctions on Ismail Haniya, who was named head of Hamas in May 2017.
Hamas has been on the US terror blacklist since 1997 but Turkey's ruling Islamic-rooted Justice and Development Party has friendly ties with the movement.
"We are concerned that this decision of the US administration, which disregards the realities on the ground, could undermine the Middle East peace process, including the efforts for intra-Palestinian peace and reconciliation," Hami Aksoy, the Turkish foreign ministry spokesman, said in a statement.
"We also hope that the decision will not have a negative impact on our country's humanitarian assistance and economic development activities towards Gaza."
Aksoy said the move overlooked the fact that Hamas is "an important reality of Palestinian political life".
Haniya is now on the US Treasury sanctions blacklist, which freezes any US-based assets he may have and bans any US person or company from doing business with him.
Washington's decision comes as ties between the Americans and Palestinians have worsened since US Donald Trump recognised Jerusalem as Israel's capital last year.
Turkish President Recep Tayyip Erdogan, a fervent supporter of Palestinians, sought to lead Islamic condemnation of Trump's Jerusalem plan late last year. At one point, he called a summit of Muslim nations in Istanbul in response to the move.
Palestinian Foreign Minister Riad al-Malki will visit Turkey today and tomorrow and hold talks with his Turkish counterpart Mevlut Cavusoglu.
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