"The use of lethal force against peaceful demonstrators and their arbitrary arrests are unacceptable," said a statement from UN Secretary-General's office.
Ban spoke with Bahrain's King Hamad bin Issa Al Khalifa and expressed deep concern over reports of "excessive and indiscriminate use of force" against unarmed civilians and medical personnel.
The abuses allegedly include killings, withholding treatment from the wounded and attacks on doctors as they try to help injured protesters. The government denies the claims.
"The Secretary-General noted that such actions could be in breach of international humanitarian and human rights law," said the statement.
Bahrain''s Foreign Minister Sheikh Khaled Al Khalifa has defended the state of emergency that has been declared in the country, which has banned public gatherings and protests.
In the UK, rights groups have raised objection to King Khalifa's invitation to the royal wedding of Prince William and Kate Middleton.
On reports of killing of protesters in Syria, it said, "It is the responsibility of the Government in Syria to listen to the legitimate aspirations of the people and address them through inclusive political dialogue and genuine reforms, not repression."
On Yemen, Ban condemned the use of live ammunition against protesters by security forces in the capital Sana'a, which killed over 46 people.
"The Secretary-General is deeply troubled by the continuing violence and instability in Yemen," the statement said.
"He calls on all to desist from any provocative acts that might lead to further violence," it said.