Eritrean troops fought alongside the Ethiopian military and allied militias during a two-year conflict against rebellious Tigray forces.
They have been accused by local residents and rights groups of widespread abuses, including killings and rapes - allegations Eritrean officials have denied. Residents and foreign diplomats say many Eritrean troops remain in Tigray despite having pulled back from several major towns.
Isaias made a rare appearance before the international media, taking part in a joint news conference with Kenyan President William Ruto during a visit to Nairobi.
"You talk about the withdrawal or no withdrawal, we've said this is nonsense," he said in response to a reporter's question. "Don't provoke us to come to a misunderstanding. Why are we bothered about Eritrean troops who are there or not there, come out or not come out?"
A peace agreement in November between the Ethiopian government and the Tigray forces ended hostilities that killed tens of thousands of people. It also required the withdrawal of all outside forces from Tigray.
Eritrea was not party to the truce. A senior U.S. official said last month that Eritrean troops were still in Tigray.
Tigray residents and rights groups accused Eritrean forces of a litany of abuses during the war, including killing hundreds of civilians in the town of Axum during a 24-hour period in November 2020 and gang-raping women and forcing them into sexual slavery.
Isaias echoed his government's earlier denials of abuses. "Everybody talking about human rights violations here and there - rape, looting - this is a fantasy," he said.
He declined to answer questions about the number of Eritrean troops killed in the war and whether he had plans in place for his succession. He has been president since Eritrean independence in 1993. (Reporting by Ayenat Mersie Editing by James Macharia Chege, Aaron Ross and Frances Kerry)