Israeli troops shot dead a Palestinian farmer near the border in northern Gaza in the first deadly shooting since an August truce ended a 50-day war, medics say.

Ashraf al-Qudra, Gaza's emergency services spokesman, identified the dead man on Sunday as Fadel Mohammed Halawa, 32, saying the bullet hit him in the back.

He said the bullet appeared to have been fired from a nearby army watchtower at a man who was farming land near the border fence.

One of Halawa's relatives said he had been searching for songbirds, which nest in trees near the Israeli border and command high prices in Gaza markets.

The Israeli army said two Palestinians had approached the border fence and had ignored calls to halt, prompting troops to fire warning shots in the air.

"Once they didn't comply, they fired towards their lower extremities. There was one hit," a spokeswoman said.

The army did not confirm the man's death and had no comment on reports he was shot in back.

If the troops' responsibility is confirmed, this would be the first time a Palestinian from Gaza had been killed by Israeli fire since a seven-week war between Israel and Hamas fighters ended with an Egyptian-brokered ceasefire on August 26.

Following the initial truce agreement, the sides were supposed to have resumed talks on some of the thornier outstanding issues within a month, but the deadline has been repeatedly delayed.

Israeli policeman charged

In another development on Sunday, Israeli prosecutors charged a policeman in the fatal shooting of a teenage Palestinian protester, accusing him of deliberately switching his non-lethal rubber bullets with the live round that killed the youth.

The prosecutors' decision to level a charge of manslaughter rather than murder drew criticism from the boy's father, who said the evidence showed the killing was pre-meditated.

Nadim Nuwara, 17, was shot during a demonstration in May at which Palestinians hurled stones at Israeli forces in the occupied West Bank.

A second teenage protester was killed there but Israel has made no arrest in that case, citing lack of evidence as an autopsy was not carried out.

CCTV footage suggested neither youth posed any immediate threat to the troops stationed some 64 metres away.

Their deaths stoked Palestinian fury at Israel that has simmered since US-sponsored peace negotiations collapsed in April. The accused, a member of the paramilitary border police whose name was not released, was arrested on November 12.

An indictment filed at Jerusalem District Court said the policeman had slipped a live bullet into his ammunition clip, which was meant to hold only non-lethal blank rounds with which to propel rubber bullets mounted separately on the rifle muzzle.

Manslaughter, a charge associated with unintentional killings, carries a maximum 20-year prison term in Israel though judges can hand down lighter sentences. Murder usually carries a life term.

"All indications show the killing was deliberate and pre-mediated. It was not random fire," Nuwara's father, Siam, told Reuters. "A manslaughter charge is unacceptable. What sentence might he get if the charge is manslaughter?"

The policeman has previously denied firing live ammunition, saying he used rubber bullets only in the incident outside Israel's Ofer Prison, near the Palestinian town of Beitunia. He has yet to plead to Sunday's charge.