Two Iranian warships leave Port Sudan on Wednesday after a three day stay.
The first ever visit by Iranian naval vessels comes less than a week after Khartoum accused Israel of attacking an arms factory in the capital.
Four people were killed after a blaze broke out which Sudanese authorities say was caused by an Israeli air strike.
Israel has not commented on the fire in the Sudanese capital.
Speaking to the media at Port Sudan, the Iranian military attache to Sudan repeated the accusations, harshly speaking out against Israel.
A Sudan military spokesman, however, said the Iranian naval visit was not intended to show aggression towards any particular nation.
(SOUNDBITE) (Arabic) SUDANESE ARMED FORCES SPOKESPERSON, COLONEL AL-SAWARMI KHALID SAAD, SAYING:
"It is not targeted at anyone and is not intended as a hostile act, but it is an action aimed at improving political and diplomatic actions, and the joint security for both Sudan and the Republic of Iran maritime forces."
Sudan, with close ties to Iran, has long been seen by Israel as a conduit for weapons smuggled to the Hamas-ruled Gaza Strip, via the Egyptian Sinai desert.
