A rebel spokesman denied any link with Israel and said the charge was an attempt to stir up Muslim public opinion.
Sudanese Foreign Minister Mustafa Osman Ismail told reporters in Cairo some leaders of the rebel Justice and Equality Movement (JEM) had split from the group two days ago over ties between its leadership and Israel.
The Islamist government in Khartoum has said 210 JEM rebels surrendered their arms in the Chadian-Sudanese border town of Tine on Friday, a report which JEM denied.
Ismail said those who had broken away from the group, "confirmed that the leadership of the movement make regular visits to Israel".
JEM, one of two Darfur rebel groups, denied the accusation and said none of its leaders had split from the group.
"There is no relationship between the movement and Israel and I have no knowledge of any intention that there should be a relationship. It is lies on the part of the government," JEM Secretary-General Bahar Idriss Abu Garda told Reuters.
"The government is striving to mislead Arab and Islamic public opinion," he said.