One was killed, 28 people were injured in the Egyptian city of Port Said overnight in clashes involving supporters of ousted president Mohamed Morsi, Aswat Masriya news website reported.

An 18-year-old, Mohamed Attia, was shot dead by unknown assailants, according to deputy health minister Helmi El-Afny in Port Said.

Witnesses and state news agency MENA said Morsi supporters had opened fire during the funeral of a fellow loyalist, but the ousted president's Muslim Brotherhood group denied the claims.

The news agency, citing a local hospital official, said 15 people were wounded by live fire after Morsi supporters began shooting during the funeral in the Suez Canal city.

"Mourners at the funeral of a young supporter of Morsi... opened fire on the Saint George church during the funeral and burned a police car in front of it," Port Said resident Al-Tabei Faruq told AFP.

"Morsi's supporters smashed the windows of shops that were displaying pictures of General Sisi," he added of Abdel Fattah al-Sisi, head of the army that ousted Morsi on July 3.

But Urfa Abu Salmiya, a spokesman for the Brotherhood's Freedom and Justice Party, denied that Morsi supporters started the clashes.

"Some youths attacked mourners at the funeral," he said.

A medical source in Port Said's Al-Amiri hospital said five people were being treated there "including two in a critical condition, with bullet wounds to the neck and chest".

Hundreds of Morsi supporters have been holding a sit-in at Port Said's Al-Tawhid mosque since his removal by the military following mass protests against him.

On Saturday, at least 72 people were killed in violence at a similar sit-in in Cairo.

Port Said has been a flashpoint for tensions since February 2012, when at least 74 people were killed in a football stadium riot.