Sudan said the expulsion of the workers from the International Organization for Migration (IOM) was not related to the genocide accusation.
Khartoum expelled 13 foreign aid organizations last year after the court issued an initial arrest warrant in March 2009 against Bashir for war crimes and crimes against humanity in the Darfur conflict.
UN officials say as many as 300,000 people have died and over 2.7 million been driven from their homes in seven years of ethnic and politically motivated violence in Darfur, a remote region of Western Sudan. Khartoum says 10,000 have died.
"We have declared two employees of IOM persona non grata. This is absolutely not related to the International Criminal Court," a Sudanese Foreign Ministry spokesman said.
"The reason is that they practiced many activities that were not related to their duties and their mandate," Moawia Osman Khalid told Reuters without specifying those activities.
The IOM headquarters in Geneva confirmed the expulsions and said the Sudanese government had given it no explanation for the decision. The two international staffers had been working with refugees in Darfur, it said in a statement.
"We regret very much what they have done," IOM chief of mission in Khartoum, Jill Helke, said, adding the pair would leave on Saturday.
The ICC warrant issued against Bashir on Monday was based on three counts of genocide, five of crimes against humanity, including murder, extermination, forcible transfer, torture and rape, and two of war crimes.
Earlier, a Khartoum court jailed three opposition journalists after finding them guilty of destabilizing the constitutional system, their lawyer said Thursday, in the latest sign of a media crackdown.
A judge sentenced Abuzar Al-Amin, deputy editor in chief of the daily Rai Al-Shaab, to five years in prison, and two other journalists, Ashraf Abdelaziz and Al-Tahir Abu Jawhara, to two years each, said the lawyer.
"It is not reasonable to put journalists in prison for what they write with their pens. We will appeal," defense counsel Abdel Moneim Osman, said.
