The newspaper said in a report published Saturday that it obtained audio recordings in which an Egyptian intelligence officer, speaking with influential talk show hosts, asked them to downplay the significance of US President Donald Trump's decision.
The New York Times said Saturday Cairo allegedly instructed talk show hosts to persuade viewers to accept the US move.
"Egypt's diplomatic stance will not be presented through leaks of doubtful credibility, but rather by the president [Abded Fattah al-Sissi] and the foreign minister [Sameh Shoukry] and official statements and all of these parties have made their resolute position on Jerusalem and the Palestinian issue clear, and this has been translated into deeds and votes at United Nations institutions despite threats from the United States", the Egyptian statement said on Sunday, according to Haaretz.
The debate caught fire when The New York Times published a report on Saturday titled "Tapes Reveal Egyptian Leaders' Tacit Acceptance of Jerusalem Move" by David D. Kirkpatrick, the Times' London-based global correspondent. The Times said the recordings all appeared to match public recordings of the hosts' voices and that one of the hosts, Azmi Megahed, confirmed during an interview with the newspaper the authenticity of the recording in which he is heard agreeing with Kholi.
A statement by the State Information Service said: "Egypt's positions on worldwide issues are not derived from alleged leaks from an anonymous source".
Azmy Megahed, who was the fourth host on the list, denied to SIS knowing who Ashral el-Kholi is. "We have enough on our plate".
However, in the recordings released by Mekameleen, el-Kholi can be heard telling one of the hosts that he was calling to lay out "the stance of Egypt's national security apparatus and what it stands to benefit from in this matter of announcing Jerusalem to be the capital of Israel".
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"The point that is unsafe for us is the intifada issue", Kholi added. "Hamas would be reborn once more", he reportedly said. However, he told the hosts not to toughly condemn the move and persuade the viewers to accept the decision because a strife with Israel is not "in Egypt's national interest".
He added, according to the Times, "At the end of the day, later on, Jerusalem won't be much different from Ramallah".
Egypt was among one of the first countries to criticise the decision by US President Donald Trump, which prompted widespread global condemnation and deadly protests in the occupied Palestinian territories.
The government statement also said there is no evidence that al-Kholi is actually a member of the security services.
"There is a political decision to recognize Jerusalem as the capital of Israel and we will strive to reach an worldwide political decision to recognize a Palestinian state ... with (eastern) Jerusalem as its capital", Safadi said.
The statement noted that two of the talk show hosts mentioned in the report no longer have shows and never presented any news regarding the Jerusalem decision.
One of the phone calls was also to well-known Egyptian actor and singer, Yousra, who heeded his advice.