Earlier, Al Jazeera's Nour Odeh reported that among those arrested by Hamas were women and some prominent members of the Palestine Liberation Organisation (PLO), notably Zakaria Agha, who is a member of the PLO executive committee.
In Rafah, in the south of the territory, Hamas police fired bullets in the air to break up a gathering of would-be worshippers and made further arrests.
Executive Force members also used batons to disperse protesters in the north.
The demonstrators were PLO supporters, including Fatah, who held open-air prayers in Gaza in protest at Hamas' takeover of the strip.
Palestinian groups affiliated to PLO, of which Hamas is not a member, later issued a statement calling on their members to observe a strike on Sunday and demanding that Hamas apologise for its actions and release all detained protesters.
If it goes ahead it will be the first general strike since the Hamas takeover.
It is the fourth week in a row that politically motivated Friday payers were attempted.
Earlier on Friday, Mahmud Abbas, Palestinian president and leader of rival Fatah, appealed to worshippers to avoid "friction or clashes with the putschists and their militias who do not hesitate to invoke the worst kind of repression.
|Abbas joined Friday prayers in Ramallah in 'solidarity with the people of Gaza' [AFP]|
"We are trying to avoid any bloodshed and the putschists must not be provoked," he said in a message via the official news agency.
Around 750 Fatah supporters gathered with Abbas in Ramallah for prayers in solidarity with Fatah in Gaza as thousands of Palestinians gathered at similar prayer rallies elsewhere in the West Bank.
Riyad Malki, Palestinian information minister, likened the Gaza protests to the beginnings of Palestinian uprisings against Israeli rule in 1987 and 2000.
"What we have seen today in Gaza is a new intifada against the Hamas occupation," he said.
Marwan Bishara, Al Jazeera's analyst, said: "This is not an intifada ... This is a power struggle between occupied people, over who will control the prison (Gaza) - Fatah or Hamas."
Hamas leaders, Gaza's effective rulers, have banned public prayers saying they are politicised and aimed at deepening divisions in Palestinian society.
Islam Shahwan, spokesperson for the Hamas Executive Force, said: "We will not allow anyone to break the decision of the government and we will strike with an iron fist all those who try to sabotage public order."
Odeh said a relgious ruling (fatwa) from Hamas-allied religious figures has backed the decision, calling those who attend the demonstrations "sinners".
Meanwhile, clashes between the Israeli military and Palestinian fighters show no signs of lessening.
Soldiers killed six armed Palestinians in the Gaza Strip on Thursday as they approached a military position intending to launch an attack, according to an Israeli army officer.
"Six Palestinians armed with assault rifles and grenades, who were approaching a military position in the Kissufim area, intending to attack, were killed during a combined air force and infantry action," Colonel Shlomi Dahan said.
The incursion came a day after Israel's defence minister said a broad operation inside the territory was inevitable.
Source: Al Jazeera and Agencies