Ali al-Sadig, Sudan's foreign ministry spokesman, said on Wednesday: "Nine American soldiers in four military vehicles forcibly went into the embassy after overpowering the guards and searched the embassy offices inside."
The embassy has been officially closed for more than a year after Sudanese diplomats were targeted in attacks in an effort to get Arab states to withdraw their diplomatic representation in Iraq.
But al-Sadig said two Sudanese guards still worked at the embassy.
Garver said he had no knowledge of any such raid: "We have no record of any MNF-I [Multi-National Force-Iraq] troops conducting a raid on the Sudanese embassy."
But al-Sadig said Sudan had demanded an apology from the US charge d'affaires in Khartoum, who said he would consult his headquarters before replying.
"This violates all international norms and we expect an apology," al-Sadig said.
Sudan has tense relations with the US, which has imposed stringent economic sanctions on the African nation, and lists it as a "state sponsor of terror".