Mahamat Hissene, Chad's communications minister, said on Tuesday that Sudanese troops backed by two army helicopters helped the rebels in an attack on an army post in Bakout, about 800km east of Ndjamena.
Sudan denied the allegations.
Recent rebel offensives have drawn strong international condemnation.
Ban Ki-moon, the UN secretary-general, has added his voice to those of UN Security Council and the African Union Commission in condemning the attacks.
The UN refugee agency has said that the security situation in eastern
Chad is deteriorating, but it is maintaining its presence in all 12 refugee camps in the country's east.
In February, rebels reached the edge of the presidential palace in Ndjamena after travelling for days from the east of the country.
The Chadian army responded with fire and forced the fighters back to the eastern border.
The Red Cross said more than 160 people were killed and 1,000 wounded
in that confrontation.
Last month, Sudan broke off diplomatic relations with Chad, accusing its
neighbour of supporting an attack on Sudan's capital, Khartoum, by the rebel Justice and Equality Movement, based in Darfur.
Chad responded by closing its border with Sudan and halting bilateral trade.