Iranian warships that docked in Saudi Arabia this month were part of a "training tour for students" in the Islamic republic's navy, the state news agency SPA reported on Saturday.
It said officials at Tehran's embassy in Riyadh submitted a request for two ships and a helicopter to dock at Jeddah between February 1 and 7.
"The purpose of such docking is part of a training tour for students of the Iranian Navy, rather than what has been stated by the Iranian Navy Commander Admiral Habibollah Sayari," said the English-language statement.
On February 4, Iran's Fars news agency quoted Sayari as saying the supply ship Kharg and Shaid Qandi, a destroyer, had docked in the Red Sea port after orders from Iran's supreme leader Ayatollah Ali Khamenei.
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"This mission aims to show the power of the Islamic republic of Iran on the open seas and to confront Iranophobia," Sayari said.
But Saudi Arabia said on Saturday "these approvals come within the framework of a long tradition of naval forces throughout the world, allowing passage and docking within international conventions."
SPA said the defence ministry approved the visit because the kingdom was keen to sustain strong ties "with all brotherly and friendly countries."
Iran's navy has been boosting its presence in international waters since last year, deploying vessels in the Indian Ocean and Gulf of Aden on missions to protect Iranian ships from Somali pirates.
After leaving Saudi waters, the two Iranian vessels transited the Suez Canal and entered the Mediterranean before docking at Tartus in Syria to help "train the Syrian navy."
Ties between Tehran and Riyadh, which have long been strained, deteriorated in late 2011 following US allegations that a foiled plot to assassinate the Saudi ambassador to Washington had been hatched in Tehran.