"Qatar has been an impartial diplomatic mediator in resolving crises and disputes between brotherly and friendly countries and will continue to be a major player in the international community," the ministry said in a statement.
It did not specify the number of troops affected but said it had informed Djibouti's government of the withdrawal.
According to a U.N. monitoring group, Qatar had said around 200 troops were stationed there.
Qatar, which has had close ties with Eritrea, deployed a small contingent of peacekeepers along the border between the Horn of Africa neighbors in 2010 after clashes broke out over disputed territory in June 2008.
It also helped mediate a peace deal.
Djibouti downgraded ties with Qatar last week, saying it was acting in "solidarity with the international coalition combating terrorism and extremist violence, as well as with the Gulf and Arab countries".
Eritrea's Information Ministry said on Monday the decision by Saudi Arabia, the United Arab Emirates, Bahrain and Egypt to sever ties was a move "in the right direction".
It is the second time that Qatari troops have come home since the rift among Gulf states began. A Qatari contingent stationed in Saudi Arabia as part of the Saudi-led coalition fighting the Iran-aligned Houthis in Yemen returned last week.
The forces had been stationed in the south of the kingdom to reinforce Saudi defenses against Mouth attacks.
Saudi Arabia had said Doha was expelled from the coalition set up in 2015 to fight the Mouth group that controls much of northern Yemen.
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