The Sovereign Council, its highest ruling body, sought to play down the importance of the visit, saying it was not political.
"We did not announce it at the time because it was not a major visit or of a political nature," council spokesman Mohamed al-Faki Suleiman told the US-based pan-Arab channel Al-Hurra on Sunday.
He said the visit "was of a technical and military nature".
Read also: How US blackmail pushed Sudan to normalise ties with Israel
Sudan in October became the third Arab country in as many months to announce a normalisation deal with Israel, after the UAE and Bahrain.
Suleiman said "discussions with the Israeli side are on hold as there were political and economic obligations that were not respected", without elaborating.
That may have been a reference to Sudan's removal from a US "state sponsors of terrorism" blacklist, which would need the backing of a vote in Congress.
Israel announced on November 23 that it had sent its first delegation to Sudan after the deal on normalisation.
But the following day Khartoum denied knowledge of the visit.
Normalisation agreements between Arab states and Israel were slammed by the Palestinians as a "betrayal" for breaking with years of Arab League policy on the Israeli-Palestinian conflict.
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