A senior Palestinian diplomat at the UN said on Tuesday that Mahmoud al-Zahar had made the reference in a letter he sent to the UN secretary-general this week.
But al-Zahar told Reuters that "such a sentence was not used in the letter".
A copy of the letter seen by Reuters also showed no reference to a two-state solution.
A Hamas official in Gaza told Reuters the wrong letter had been sent. The official said al-Zahar made changes to an initial draft of the letter, such as deleting references to the two-state solution. The older version was mistakenly sent.
A spokesman for Kofi Annan meanwhile said that the UN chief was withholding comment on al-Zahar's letter.
"That letter is being studied. We don't have any further comment at this stage," spokesman Stephane Dujarric said on Wednesday.
A UN official said Annan appeared to be in a bind because of al-Zahar's retraction of the unprecedented reference to a "two-state solution" to the Middle East conflict.
Hamas, which swept parliamentary elections in January, is sworn to Israel's destruction. It says talks with Israel will be a waste of time.
Israel calls Hamas a terrorist organisation and has vowed not to negotiate with the group.
Despite not referring to a two-state solution, al-Zahar's letter to Annan was conciliatory for a Hamas leader with reputation as a hardliner.
Al-Zahar said his government wanted "to work with the United Nations and countries of the world ... to achieve regional peace and stability based on a comprehensive and just solution."
"We hope some countries will reconsider their positions and hasty decisions especially regarding stopping aid and the use of the language of threats instead of dialogue," the letter added.
"We speak about a Palestinian state, fully sovereign, with Jerusalem as its capital and on Palestinian lands occupied in 1967 as an interim solution. This is one item on the government agenda, but recognition of Israel is not"
Israel and the US have sought to isolate the Hamas government.
The Quartet of Middle East mediators - the United Nations, the United States, the European Union and Russia - has also said that aid will be cut if Hamas does not recognise Israel, renounce violence and accept interim peace agreements.
Riyad Mansour, the UN Observer for Palestine, speaking at the world body's headquarters on Tuesday, said that the choice of wording in al-Zahar's letter was important, hinting at an evolution in Hamas thinking.
Mansour said the letter also referred to the Palestinian hope of wanting to live in peace "side by side with our neighbours", which could have implied Israel.
Mushir al-Masri, a Hamas lawmaker, said recognising Israel was not up for debate, although he restated the group's offer of a long-term truce if Israel was to fully withdraw from the land captured in the 1967 war.
Israel has dismissed such an offer as a non-starter.
"We speak about a Palestinian state, fully sovereign, with Jerusalem as its capital and on Palestinian lands occupied in 1967, as an interim solution. This is one item on the government agenda, but recognition of Israel is not," he told Reuters.