On 8 April, the Chadian government accused Khartoum of arming and financing a force of 3,000 Chadian rebels which had allegedly gathered 25 km from the frontier near the Sudanese border town of El Geneina.
President Idriss Deby, who was instrumental in launching peace talks between three rebel movements in Darfur and the Sudanese government last year, threatened to withdraw as a mediator in the conflict.
A week later, the Chadian consul in the Sudanese border town of El Geneina was attacked and wounded by unidentified gunmen. His car was sprayed with bullets on 14 April as he was driving towards the Chadian border.
But the response to Chad's protests from the Islamic government in Khartoum was swift and decisive.
Two ministers were dispatched as special envoys in two separate missions to N'Djamena to pacify the ruffled Chadian leader.
On 16 April - less than two weeks after the affair blew up - Deby announced that the damage to bilateral relations had been repaired.
He said that Khartoum had given assurances that it would remove the armed men from the border and that if it did so, Chad would resume its role as a mediator in international efforts to negotiate an end to the two-year-old Darfur conflict.
Relations between Chad and Sudan have been strained ever since the Darfur conflict erupted in February 2003.
On the one hand, Deby owes a debt of political gratitude to Sudanese President Omar Hassan El Bashir for supporting his faction of the army when it fought its way to power in a civil war in 1990.
On the other Deby, is a man of torn loyalties in the Darfur conflict.
He belongs to the Zaghawa ethnic group which lives on both sides of the border and is strongly engaged in fighting the Sudanese government and its Janjawid militia allies in Darfur.
Diplomats and political analysts in Chad say Deby faces strong pressure from many of his family and clansmen to actively help his Zaghawa brothers on the Sudanese side of the border.
But Deby knows that to do so would invite active Sudanese support for Chadian rebel groups which have been sporadically active on the desert fringes of the country ever since he came to power 15 years ago.
And diplomats say Khartoum is aware that direct Chadian support for the rebels in Darfur would simply escalate the conflict in the vast semi-desert region, which has already driven nearly two million people from their homes.
According to relief workers in the frontier region, whatever may be said by political leaders in the distant capitals, armed men are constantly criss-crossing the remote and sparsely populated border.
One foreign aid official contacted by telephone in El Geneina, told IRIN that there was nothing new about Sudan hosting Chadian rebels or Darfur rebels crossing the border into Chad, 40 km to the west.
"There is nothing new about the fact that one country shelters rebels from the other," he said. "For more than 20 years militias opposed to the government in Chad have enjoyed well-established bases in Sudan, just as the SLA (Sudan Liberation Army) has bases in Chad."
"Now, whether there are 1,000, 2000 or 3,000 rebels here, I don't know. But it is clear that just recently the Chadian opposition has been finding refuge in Sudan."
Aid workers looking after 200,000 refugees from Darfur on the Chadian side of the frontier said they had noticed a strengthening of border patrols by Chadian police and soldiers, but there had been no sign of any other unusual activity.
"Our troops have been reinforced along the frontier and we are in a state of alert," confirmed Colonel Hamat Bong Aware, a senior commander of the Chadian army in Abeche.
France, which has a military garrison stationed in Chad has been helping Chadian security forces to patrol the Sudanese border for several months. A French officer involved in supervising these frontier patrols told IRIN there had been no sign of rebel forces of any description on the Chadian side of the border.
But another security source, involved in the protection of aid workers in eastern Chad, said intelligence reports indicated that armed opponents of Deby's regime were indeed massing inside Sudan.
He noted that recently there had been a tendency for these small and disparate groups to coalesce into a stronger and more united rebel movement.
"Political and military movements which have bases in Sudanese territory are establishing themselves along the border, while the government closes its eyes," the source told IRIN.
"Going by the information available, we can estimate that there are about 10,000 rebels. We have identified about 16 different factions, the most important of which is the National Renaissance Alliance (ANR) run by a certain Captain Garma. These movements are spread throughout Darfur, but particularly around towns like El Fasher and El Geneina."
Nevertheless one western diplomat in N'Djamena was sceptical that the number of Chadian rebels in Sudan amounted to anything more than a few hundred men.
"I reckon Deby has been exaggerating (the number of rebels)," the diplomat told IRIN. "Had there really been 3,000 men out there he would have emptied the capital of soldiers. Remember that when he himself took power in 1990, it was with a force of less than 1,000 men."
Ahmat Allami, a special adviser of President Deby, who has been closely involved in Chadian efforts to mediate between Khartoum and the Darfur rebels, said the Chadian government first heard about thousands of armed Chadian dissidents massing near El Geneina from a confidential report submitted by African Union military observers in the area.
But he added: "The Sudanese authorities seem to have proved their goodwill by sending two different delegations to N'Djamena and these have pledged to dismantle the rebel elements on their territory."
A spokesman for the 2,260 AU military observers in Darfur, declined to confirm the existence of the confidential report cited by Allami. "The African Union has got nothing to do with these rumours that have been put about," he told IRIN.