Ban called King Hamad on Thursday to express his "deepest concern" about the use of force, which allegedly includes security forces preventing doctors from treating injured protesters in the tiny Gulf state.
The secretary general "expressed his deepest concern over reports of excessive and indiscriminate use of force by the security forces and police in Bahrain against unarmed civilians, including, allegedly, against medical personnel," a UN statement said.
He also "noted that such actions could be in breach of international humanitarian and human rights law."
The UN chief spoke out following a bloody crackdown on Shiite-led protesters by the US-backed Sunni Muslim rulers. Bahrain is home to the US Fifth Fleet.
The violence in the strategic kingdom has alarmed Washington and sparked furious condemnation from Iran, Shiite leaders in Iraq and the Hezbollah militia in Lebanon.
Valerie Amos, the UN's deputy secretary general for humanitarian affairs, earlier urged security forces "to refrain from excessive use of force, and to respect medical facilities and ensure the treatment of wounded persons."
UN rights chief Navi Pillay earlier Thursday said any takeover by the security forces of hospitals and medical facilities was a "blatant violation of international law."
"There are reports of arbitrary arrests, killings, beatings of protesters and of medical personnel, and of the takeover of hospitals and medical centres by various security forces," she said.
"This is shocking and illegal conduct."
Dissidents had been rounded up at gunpoint in midnight raids and armed police stood outside Manama's main hospital on Thursday, amid reports the authorities were beating doctors and denying treatment to the wounded.
Unbowed, the Shiite-led opposition vowed to press on with "peaceful" demonstrations, undeterred by the deadly military force against them.
"We will not give up to the army," said Shiite cleric Sheikh Ali Salman, the head of Al-Wefaq association. "We insist on the peaceful aspect of our activities and we shall not be dragged into... confrontations."
The opposition called for fresh protests "within the praying areas" rather than out on the streets after Muslim weekly prayers on Friday and for sit-ins on Saturday.
Fresh clashes erupted in at least one Shiite village outside the capital, after five people were killed on Wednesday when security forces crushed a month-old pro-democracy sit-in at Manama's Pearl Square.
Five hardline Shiite activists and one Sunni dissident were arrested after the army imposed a curfew on parts of Manama using its powers under newly imposed martial law, opposition sources said.
Bahrain's military confirmed it had arrested a number of people for crimes including sedition, murder and having contact with foreign states, but gave no details.
Opposition MP Khalil al-Marzouk said that Doctor Ali al-Ekri, who had been accused on state TV of spreading "fabrications" about conditions at Salmaniya hospital, was arrested there on Thursday.
Security forces firing tear gas and shotguns cleared out a pro-democracy tent city at Pearl Square on Wednesday in the worst day of violence since activists took to the streets last month.
The opposition said three demonstrators were killed in the raid, while the government said two police died in hit-and-run attacks by opposition motorists.
US President Barack Obama, whose country is a close ally of Bahrain, called King Hamad to express "deep concern," while British Prime Minister David Cameron urged the monarch to pursue "reform, not repression."
The main opposition is demanding a constitutional monarchy, the resignation of the government and an end to repression in Bahrain.
King Hamad declared a three-month state of emergency on Tuesday a day after more than 1,000 armoured troops from Saudi Arabia and the United Arab Emirates entered Bahrain to help restore security.
The sectarian tensions have given rise to fears among Bahrain's Sunni-led Arab neighbours that Iran, the Shiite power a short boat ride away across the Gulf, is seeking to foment unrest in the kingdom.
US Secretary of State Hillary Clinton called the situation in Bahrain "alarming" and criticised Washington's Gulf state allies for heading down "the wrong track" of military intervention.
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