Foreign Minister Mohammad Javad Zarif dismissed them as "failed lies".
He claimed they were published "just in time" for the American Israel Public Affairs Committee (AIPAC) conference, which took place earlier this week.
On Wednesday, Israel's military said it had found the rockets on a ship it seized in the Red Sea off Sudan.
The Klos-C, a Panamanian-flagged vessel, is currently being escorted to the southern Israeli port of Eilat, and is expected to arrive on Saturday. Its 17-member crew were apparently unaware of their cargo.
The Klos-C was transporting dozens of M-302 rockets, which have a range of 150km to 200km (93-124 miles), Israeli military spokesman Brig-Gen Moti Almoz said.
"The ship may be carrying other weapons as well, but we can only know this when it reaches Eilat."
"There is clear and unequivocal information that this came from Iran."
On Wednesday, the Israeli military said it had tracked the weapons for several months as they were flown from Damascus to Tehran and then taken to a port in southern Iran.
From there, it added, they were loaded on to the KLOS-C, which sailed to Iraq, where containers of cement were added. The ship was eventually intercepted while on its way to Sudan.
On Thursday, Mr Zarif rejected the allegations and questioned why they had surfaced just after the conference a pro-Israel US lobby group.
"An Iranian ship carrying arms for Gaza," he wrote on Twitter. "Captured just in time for annual AIPAC anti-Iran campaign. Amazing Coincidence! Or same failed lies."
A spokesman for Hamas, the militant Palestinian Islamist movement that governs Gaza, said they were a "silly joke".
Israel has long accused Iran of arming groups such as Hamas.
More than 60 rockets fired from the Gaza Strip have hit Israel since the start of last year, Israel says.
Hamas denies that it has fired any rockets since a 2012 ceasefire agreement with Israel, with other Gaza-based groups claiming responsibility. However, Israel says it hold Hamas responsible for any attacks from Gaza and has repeatedly launched deadly air strikes.
During a visit to California on Wednesday, Israeli Prime Minister Benjamin Netanyahu said the discovery of the shipment had revealed "the true face of Iran" to world powers attempting to negotiate a comprehensive agreement on its controversial nuclear programme.
"Iran has been exposed for what it is," he told reporters. "It smiles in the Geneva talks about its own nuclear ambitions, gives soothing words, and as they're doing that, they're shipping these deadly weapons to the world's worst terrorists."
In a speech at the AIPAC conference on Tuesday, Mr Netanyahu had reiterated his unhappiness with the prospect of a long-term deal that would allow Iran to continue enriching uranium and engaging in other activities that might allow it to develop nuclear weapons.
At a news conference in Jakarta on Thursday, Mr Zarif insisted that Iran's nuclear programme was solely for peaceful purposes.
"I do not believe dismantling of this programme is helpful to the cause of non-proliferation because Iran has technology, Iran has the scientists, Iran has the capability," he said.
"So the best way to ensure that these scientists, and the technology, and the capability, and the workshop are designed only for peaceful purposes and used exclusively for peaceful purposes is to have them out in the open under international monitoring," Iran's foreign minister added.

Lukasz Robert Pawlowski of Pembroke Dock, appeared for sentence at the Pembrokeshire court on Wednesday after pleading guilty to sexual assault.
He was airlifted to Swansea's Morriston Hospital and is said to be recovering.
Dyfed-Powys Police confirmed they have arrested a 33-year-old man on suspicion of possession of an article with a blade or point.
It is understood he lost consciousness and bled heavily after cutting himself.
The court was closed after the incident but reopened on Thursday.

Michael Higdon scored what proved to be the decisive goal, heading home Lee Vaughan's cross just before the hour.
Torquay almost grabbed a late equaliser when Luke Young's 25-yard free-kick was saved by Scott Davies, but Rovers held onto the lead to move three points clear in the final play-off position.
The Gulls remain in 18th with a three-point cushion from the division's relegation places.
Iran has rejected Israeli allegations that it was behind a shipment of Syrian-made rockets intended for Palestinian militants in Gaza.
[NEXT_CONCEPT]
A sex attacker who cut his own throat in the dock at Haverfordwest Magistrates' Court has been arrested.
[NEXT_CONCEPT]
Tranmere consolidated their play-off position with a narrow win at Torquay.