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Ambassador Fawaz al-Aytan and members of his security detail were abducted and his driver was injured, Jordan's Foreign Ministry said. Libyan state news agency LANA reported the driver, a Moroccan national, was shot during the kidnapping.
A spokesman for the Libyan Ministry of Foreign Affairs said masked gunmen in two vehicles ambushed the ambassador's convoy and whisked away al-Aytan.
A diplomatic source said the motive appeared to be to swap the ambassador for the release of a Libyan from a Jordanian jail.
The prime ministers and foreign ministers of Jordan and Libya discussed the situation in phone calls on Tuesday, LANA and Jordan's state news agency Petra reported.
Jordanian Foreign Minister Nasser Judeh said the kidnappers had not contacted his government, but he held them responsible for the safety of the ambassador.
"Through our permanent mission in New York, we have asked the U.N. Security Council to issue a statement condemning this unacceptable act that targeted Jordan and its diplomatic representation in Libya," Judeh told Petra.
In a separate incident, the U.S. Embassy in Tripoli said Tuesday one of its locally hired employees was abducted. Later, a senior Obama administration official said the woman, who worked for the embassy as a bodyguard, had been located.
There appeared to be no connection to the embassy, and the incident occurred after business hours when the woman was with her boyfriend in his car, another senior administration official said.
The woman escaped, flagged down a truck and was taken to a hospital, where the ambassador met with her, the official said.
A diplomatic source earlier told CNN the employee was believed to have disappeared Monday night at a checkpoint.
After the Jordanian ambassador was abducted, Jordan's national airlines, Royal Jordanian, canceled its daily flight to Tripoli.
"Royal Jordanian is closely monitoring the situation in Libya following news that Jordan's ambassador to Libya … was kidnapped Tuesday morning. The airline will take the appropriate decision in regard to its operations to Libya," the airline said on its website.
Royal Jordanian runs 10 flights a week to Tripoli, four to Benghazi and two to Misrata.
Militia groups have routinely targeted and intimidated officials in the fractured nation.
On Sunday, Libya's newly appointed Prime Minister Abdullah al-Thinni stepped down after he and his family were attacked.
Al-Thinni was with his family when his convoy came under attack by militia members near where he lives in Tripoli, a neighborhood resident told CNN.
After they escaped and entered the neighborhood near Tripoli's airport road, heavy gunfire erupted in the area.
Al-Thinni said he and Cabinet members will continue their work as a caretaker government until a new prime minister is chosen by the General National Congress, the country's interim parliament.
In October of last year, the country's former prime minister, Ali Zeidan, was kidnapped briefly by a militia in the capital.
So far this year, Egyptian diplomats, a South Korean official and a Tunisian Embassy employee have been kidnapped and later released in Tripoli.
Al-Aytan is the highest level diplomat to have been kidnapped in Libya since the 2011 revolution.
Diplomatic missions have been targeted in attacks both in Tripoli and Libya's second city Benghazi, leading all western countries to shut down their Benghazi consulates.
On September 11, 2012, U.S. Ambassador Christopher Stevens and three other Americans were killed in an attack on the American consulate in Benghazi.
In June of that year, the convoy of former British Ambassador Dominic Asquith was targeted in an attack in Benghazi that injured two British guards.
Security in Libya has deteriorated since the overthrow of Moammar Gadhafi in 2011.
Government forces have been unable to rein in the hundreds of militia groups, which have competing interests, ideologies and agendas.
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