"We will not abandon our Qatari brothers," Erdogan told members of his ruling Justice and Development (AK) Party at an iftar fast-breaking meal in Istanbul.
Speaking about a list published on Thursday claiming some charity foundations backed by Qatar had terrorist links, Erdogan said: "There is no such thing. I know those foundations."
Late on Thursday, a joint statement by Saudi Arabia, Bahrain, Egypt and the U.A.E. accused 59 individuals and 12 charity organizations in Qatar of being “linked to terror”, local media reported.
The list included the International Union of Muslim Scholars' Egyptian chairman, Yousef al-Qaradawi, and Abdullah bin Khalid, a former interior minister of Qatar.
Qatar hit back on Friday in a Foreign Ministry statement which described the accusations as “baseless” and “slanderous”.
Erdogan said he had never witnessed Doha supporting terrorism, adding Turkey "will continue to give all kinds of support to Qatar”.
On Wednesday, Turkey’s parliament ratified two deals on deploying troops to Qatar and training the Gulf nation's gendarmerie.
The deal to deploy Turkish troops in Qatar, aimed at improving the country's army and boosting military cooperation, was signed in April 2016 in Doha.
Turkey’s president also called on Saudi Arabia to remove all sanctions on Qatar and open diplomatic talks.
Meanwhile, a Friday statement from EU foreign policy chief Federica Mogherini said the bloc was calling on all sides to "avoid any further escalation and engage in a political dialogue".
Speaking earlier in Washington, U.S. Secretary of State Rex Tillerson urged Saudi Arabia and its Arab allies to ease their blockade on Qatar while calling on Doha to do more to end its alleged support of terror groups.
On Monday, five Arab countries -- Saudi Arabia, Egypt, the U.A.E., Bahrain and Yemen -- cut ties with Qatar, accusing Doha of supporting terrorism.
The escalation came two weeks after the website of Qatar’s official news agency was allegedly hacked by unknown individuals who reportedly published statements attributed to the country’s emir, Sheikh Tamim bin Hamad al-Thani.
The incident triggered a diplomatic row between Qatar and its neighbors.