In a statement on its website, Gulf Air said flights to Iran had been suspended until Monday while services to Iraq had been closed until tomorrow.
The rest of its services are operating "as normal", the airline said.
"Passengers departing from Bahrain International Airport are requested to allow themselves extra travel time to reach the airport," Gulf Air said.
The other disruptions to its network were caused by unrest in North Africa. On March 6 Gulf Air temporarily suspended flights to Alexandria in Egypt.
"Our sincere apologies for the inconvenience this may cause and thanks for your understanding," the airline said.
Bahrain's aviation industry, a critical link for the island kingdom, is being knocked amid unrest that has led to the unprecedented step of other GCC forces being asked to step in.
More than 40 airlines serve Bahrain International Airport, including the flag carrier Gulf Air and the budget airline, Bahrain Air. In the past few days protesters blocked roads leading to the capital's financial centre, where clashes have left more than 200 people injured. The disturbances have led to Gulf Air closing its downtown sales offices in Manama and Seef Mall.
On Monday, Saudi and UAE troops were sent in to Bahrain to help to establish "security and domestic stability", and a three-month state of emergency was announced by King Hamad bin Issa Al Khalifa on Tuesday.
"The unrest will impact in the short term as travellers won't be sure as to how long or how bad the situation will be," said Saj Ahmad, an analyst and aviation blogger at FBE Aerospace in London.
"Business travel shouldn't be affected too much although tourism will be hit much harder."
Tension in parts of the Mena region will affect global air travel flows, the International Air Transport Association said yesterday.
"Momentum was strong at the start of 2011 and rising business confidence points to further gains in the months ahead," it said.
"The next two months data will, however, be negatively impacted by the unrest in the Middle East and the Japanese earthquake and tsunami."
The unrest in Bahrain comes at a time when Gulf Air is picking its way through a fragile recovery and restructuring itself after years of heavy losses.
Mr Ahmad predicted the crisis would be more of a short-term than long-term worry for Bahrain's carriers. "Overall this situation won't impact long term - if the political situation is stalemated for months, passengers will see this as the status quo and start to feel a little more comfortable about flying into Bahrain," he said.