"This accord is not targeting any Gulf country," Mevlut Cavusoglu said after meeting with his Bahraini counterpart Sheikh Khalid bin Ahmed Al-Khalifa.
The purpose of the troop deployment "is to help foster security and stability across the Gulf," Cavusoglu said after talks attended by Turkish President Recep Tayyip Erdogan, who said he wanted all parties to end the standoff before the end of the Muslim holy month of Ramadan, around June 25.
Bahrain joined Saudi Arabia, the United Arab Emirates (UAE), Egypt and other states this past week in cutting ties with Qatar over what they say is the emirate's financing of extremist groups and its ties to Iran, Saudi Arabia's regional arch-rival.
The Arab countries closed air, sea and land links with Qatar, barred the emirate's planes from their airspace and ordered Qatari citizens out within 14 days.
The crisis escalated on Friday after Saudi Arabia, the UAE, Egypt and Bahrain released a list of 59 Qatari and Doha-based people and entities linked to "terrorism".
Erdogan has vowed to support Qatar, a close ally, in the dispute, even though he also wants to maintain good relations with the other Gulf states. So far, Turkey has not directly criticised Riyadh.
"Turkey will continue with its constructive actions aimed at resolving this problem. We consider the stability and security of the Gulf in the same way we consider our own stability and security," Cavusoglu said.