By Nidal al-Mughrabi

GAZA, Sept 9 (Reuters) - A one-day general strike called by President Mahmoud Abbas's Fatah faction for Sunday put Gaza shopkeepers in the precarious position of having to choose sides in its bitter rivalry with Hamas Islamists ruling the territory.

The business owners, who have abided by strike calls in the past to protest against Israeli occupation, found themselves weighing the personal cost of shutting down and angering Hamas or staying open and risking retaliation by Fatah.

"Gaza is like a ship with two captains," said one shop owner who declined to give his name. "Each captain is ordering passengers to his side of the boat. In the end, the ship will sink."

Fatah ordered the strike after violence on Friday in which Hamas security men, wielding clubs and firing in the air, broke up outdoor prayer meetings the once-dominant faction organised in defiance of a ban on such gatherings.

Standing outside an ice cream shop that remained open, a youth lit a petrol bomb and hurled it inside, setting the business ablaze, local residents said.

On Gaza's main street, about half of the shops were closed. Many people did not send their children to school.

"We attended three classes only. We stayed for half the school day -- to appease both Hamas and Fatah," one student said as he and several friends headed home early.

A pro-Fatah school principle in southern Gaza Strip said he was briefly held by Hamas security forces for closing down the school. He was later released on condition he ignore any future strike calls.

Fatah lost control of the Gaza Strip to Hamas in fighting three months ago. The Hamas administration in the territory described the strike as "pointless and an attempt to restore chaos".

Factions in the Fatah-led Palestine Liberation Organisation said anyone who defied the strike call would be viewed as an opponent of the PLO.

Some business owners told Reuters they have been warned by members of Hamas-led Executive Force their shops would be shut down permanently if they closed their doors on Sunday.

A spokesman for the Hamas administration in Gaza denied any such warnings had been issued.

After Friday's clashes in which 20 people were hurt, Reyad al-Malki, information minister of the West Bank-based Palestinian government, said: "What we saw in Gaza was the beginning of a third Intifada, against Hamas occupation".

Palestinians launched what they called two uprisings against Israeli occupation, in 1987 and 2000.

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