The death toll from a synagogue gun attack on the Tunisian island of Djerba during an annual Jewish pilgrimage has risen to five, Tunisia's TAP news agency says.

Two Jewish pilgrims and three Tunisian police guards were shot dead during the firing spree at the Ghriba synagogue on Tuesday.

Tunisian authorities opened an investigation into the attack and it was not known if the Jewish pilgrims were specifically targeted by the gunman, who was quickly slain by security guards before he could enter the synagogue complex.

Little is known about the gunman's identity.

A police guard who had been hospitalised in the immediate aftermath died from his wounds on Wednesday, according to a medical official cited by TAP, while four other members of the security forces remain hospitalised in Djerba, including one who is in critical condition.

Ghriba Synagogue committee chair Perez Trabelsi was in the synagogue during the attack and told the Associated Press of his terror "when the sound of the cartridges broke out".

"I was scared, as were most of the people gathered in the 'oukala,' a large space adjacent to the synagogue. Everyone was panicked. Many took refuge in the rooms for fear of being hit by the shots that came from outside," he said.

He was saddened that the pilgrimage to the historic synagogue that is revered in Judaism "was spoiled by those who wish Tunisia harm," he said.

The assailant, a guard affiliated with the National Guard naval centre in the port town of Aghir on Djerba, first killed a colleague with his service weapon before seizing ammunition and heading toward the Ghriba synagogue, the Tunisian Interior ministry said.

When he reached the site, he opened fire on security units stationed at the temple, who fired back, killing him before he reached the entrance, the ministry said.

Former tourism minister Rene Trabelsi told Tunisian radio Mosaique FM that he was at the Ghriba synagogue with family members during the attack.

He described the place as almost empty because most visitors had already left the site.

"The shooting was heavy and the attacker tried to enter the synagogue compound," he said.

"The counterterrorism officers, who were extremely professional, quickly blocked all exits. A carnage was thus avoided."

More pilgrims than have been seen in recent years came to Ghribi this year - about 6000 people from the United States, Canada, Australia and Europe and beyond, Trabelsi added.

Jews have been living in Djerba, a picturesque island off the southern coast of Tunisia, since 500 BC.

An annual pilgrimage at the reportedly 2500-year-old Ghriba temple, thought to be one of the world's oldest synagogues, attracts thousands of visitors from around the world.

The first Jews who arrived were said to have brought a stone from the ancient temple of Jerusalem that was destroyed by the Babylonians.

The stone is kept in a grotto at the synagogue.

Women and children descend into the grotto to place eggs scrawled with wishful messages on them.

Djerba's Jewish population is one of North Africa's biggest, although in recent years it has shrunk to 1500, down from 100,000 in the 1960s.