Eritrea has accused Sudan's authorities of arresting its nationals and closing community centres used by Eritreans in the Sudanese capital, Khartoum.
Eritrea's Foreign Ministry described the detentions as illegal and called for those held to be released.
Last month, Sudan complained to the United Nations saying that Eritrea was assisting rebels in the west of Sudan.
Two weeks ago, Ethiopia, Sudan and Yemen accused Eritrea of stirring up instability in the region.
Large numbers of Eritreans live in Sudan.
UN estimates suggest there are well over 300,000 refugees, some of whom arrived 35 years ago in the early days of Eritrea's fight for independence from Ethiopia.
The Eritrean government denies promoting instability in the region, instead accusing the Ethiopians with whom it more recently fought a two-year border war in which tens of thousands of people were killed.