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US President Donald Trump has issued a fresh warning to Iran's leadership during the state funeral ceremonies of former Supreme Leader Ayatollah Ali Khamenei, claiming the United States could eliminate the country's remaining leadership "with one shot" but would refrain from doing so to preserve the possibility of negotiations.

"They are all there. One shot and we can take them all out, but we are not going to do that because then we would have nobody to negotiate with... They are begging to make a deal," Trump told Axios.

He also said the US and Iran had agreed to pause talks until the funeral ceremonies conclude, adding that neither side would attack the other during the period.

"We gave him a week off for a funeral because we're nice," Trump said separately.

Ali Khamenei, who led Iran for 36 years, was killed on 28 February during Israeli and US strikes on Iranian targets that marked the start of the conflict. Iran began state funeral ceremonies on 4 July, with the programme set to conclude on 9 July with his burial in Mashhad after ceremonies in Tehran, Qom and the Iraqi holy cities of Najaf and Karbala.

Trump also questioned the public display of grief during the funeral after television footage showed senior Iranian leaders, including Parliament Speaker Mohammad Bagher Qalibaf and Foreign Minister Abbas Araghchi, in tears.

"I thought people hated him. Maybe it's fake tears," he said.

Iran's new Supreme Leader, Mojtaba Khamenei, remained absent from public view on Sunday as state funeral prayers were held for his father and four other family members.

Iranian state media said Mojtaba Khamenei would not attend the ceremonies because of security concerns amid continued Israeli threats.

State television showed Ali Khamenei's sons Mostafa, Meysam and Masoud attending the prayers at Tehran's Imam Khomeini Grand Mosalla alongside President Masoud Pezeshkian, Parliament Speaker Mohammad Bagher Qalibaf, Revolutionary Guard chief Ahmad Vahidi and Quds Force commander Esmail Qaani.

According to the Associated Press, the funeral prayers were led by 97-year-old Shiite cleric Ayatollah Jafar Sobhani.

Mojtaba Khamenei has not appeared in public since succeeding his father following the February attack. Reuters, citing people familiar with his inner circle, reported that he sustained facial injuries and significant injuries to one or both legs in the strike.

The funeral procession is scheduled to continue through central Tehran on Monday before moving to Qom on Tuesday. The remains will then be taken to Najaf and Karbala in Iraq before returning to Iran for a final procession and burial in Mashhad on Thursday.