The Sudanese military said it was a "normal" port call but Israeli officials have expressed concern about arms smuggling through Sudan.
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They have long accused the African country of serving as a base of support for militants from the Palestinian Islamist movement Hamas which rules the Gaza Strip.
Sudanese army spokesman Sawarmi Khaled Saad had initially announced the warship visit for November 30.
"It is part of diplomatic and military exchanges between the two countries," and will last for three days, he told reporters on Friday night.
A pair of Iranian navy vessels, the supply ship Kharg and corvette Admiral Naghdi, spent about two days at Port Sudan in late October.
The port call was accompanied by Sudanese press criticism of Saudi Arabia which lies across the Red Sea and has had tense relations with Iran for years.
Sudan's links with Iran have come under scrutiny after Khartoum accused Israel of an October 23 strike against the Yarmouk military factory in the capital, which led to speculation that Iranian weapons were stored or manufactured there.
Israel refused all comment on Sudan's accusation about the factory blast.
Iranian ships sending false signals?
Meanwhile, a new report sparked concerns that Iran is able to smuggle weapons into Syria.
The report suggested that Iranian oil tankers are sending incorrect satellite signals that confuse global tracking systems in an attempt to conceal voyages made by other ships to Syria, which, like Iran, is subject to international sanctions.
Iranian battleships in Sudan (Archives)
Large vessels such as tankers must transmit their identity and location to other ships and coastal authorities using an automatic satellite communication system, but in the last month Iranian vessels sailing in Asian seas have sent signals that took over the identity of other vessels, so the same ship appeared to be in two places at once.
"It is of course possible to manipulate or falsify information in these messages," said Richard Hurley, a senior analyst at IHS Fairplay, a maritime intelligence publisher.
At least three Iranian oil tankers are transmitting such false signals, effectively taking over the identity of Syrian-owned vessels travelling between Syria, Libya and Turkey.
All the vessels in question were registered in Tanzania.
"In the past months we witness a recurring pattern of vessels sailing the Tanzanian flag that transmit the same MMSI number (a satellite signal that provides information on a ship's identity and position)," said Windward, a firm that provides maritime analytics technology.
"This way, if one of the two vessels is engaged in legitimate maritime activities, it might be used as a 'cloaking' for the other vessel and its activities."
Responding to diplomatic pressure by the United States and European Union to drop all Iranian tankers from their registries, Tanzania's foreign minister issued a statement denying Iran's vessels had been legitimately registered.
"All the 36 Iranian ships were de-registered and hence stopped using our national flag. We have not registered any new ships as claimed," said Bernard Membe, adding that Tanzania had asked the US and EU to help investigate the Dubai-based agency that had registered the vessels.
"If we establish that this (Iranian tankers have been registered) has happened we will cancel the registrations."
Vessels without a flag cannot be insured, dock in most ports or use the vital Suez Canal shortcut between the Mediterranean and Indian Ocean.
Manipulating or turning off satellite tracking devices is not necessarily an indication that a vessel is trying to conceal illegal activity, according to International Maritime Bureau director Pottengal Mukundan.
"Vessels sometimes shut their AIS when they are going into pirate waters for example, as they wouldn't want anyone to pick up their signal because they could then be targeted by pirates," he said.
Dudi Cohen, AFP and Reuters contributed to this report
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