President Bashir said the "seized Egyptian armored vehicles" by the Sudanese forces were used by the Darfur rebels to attack two states on Friday.
Sudanese President Omar al-Bashir on Tuesday accused Egypt of arming rebel groups in the troubled Darfur region.
Speaking at a joint press conference held today in Cairo with the Austrian Chancellor, Christian Kern, Al-Sisi said: "Egypt does not conspire against any country and does not interfere in the internal relations of any country, especially Sudan".
According to al-Bashir, the Sudanese authorities had recently found Egyptian weapons in the possession of Darfurian rebels following clashes in eastern Darfur. "We fought alongside Egyptians in 1976". Egypt "did and will not intervene to destabilize Sudan or harm its people".
"We say with high [certainty] that they are Egyptian armoured vehicles", he said. The ministry reiterated that their foreign policy is anchored in respect for global law and the principles of neighborliness and non-aggression, adding that they have "special fraternal relations" with Sudan.
Also, relations between Cairo and Khartoum have suffered since July 2013, when former president Mohamed Morsi was ousted from power.
Now under Egyptian sovereignty, the disputed border regions of Halayeb and Shalateen remain a complicated matter between Egypt and Sudan, causing a restrained tension between both neighbors, experts said.
And in April, Egypt's media heavily criticized al-Bashir for a visit he paid to Ethiopia, where a major hydro-electric dam is being built on the Nile - a project Egypt fears will affect its historical access to Nile water.
Darfur has been the scene of a ferocious war between the Sudanese government and three rebel movements since 2003.
Last Month, UN envoy to Libya Martin Kobler said Darfur rebel movements have presence in war-torn Libya, a claim vehemently denied by the rebels.