Washington (CNN)With instability rising in the Middle East, President Barack Obama told Egypt's leader Tuesday that he was ending a freeze on weapons shipments to the longtime U.S. ally, a moratorium on material support that began after a bloody military-backed coup there in 2013.
Obama told Egyptian President Abdel Fattah el-Sisi in a phone call that he was lifting the holds on delivering F-16 fighter planes, Harpoon missiles and tank kits, and said he would ask Congress to continue an annual $1.3 billion in military assistance to Egypt.
The White House said the decision to resume the shipments of weapons was made in the interest of U.S. national security, though officials insist the timing isn't related to the deteriorating security situation in Yemen -- once a key U.S. ally in fighting terrorists whose government has collapsed amid advances by Iran-backed rebels.
Egypt has backed Saudi Arabia's attack on the rebels, which threatens to turn the conflict into a wider regional war.
The more than $1 billion Obama has pledged to request for Egypt makes the country the second-largest recipient of military aid. Obama told el-Sisi in their phone call that beginning in 2018. that assistance would be channeled into specific categories, including counterterrorism and security in the contested Sinai region.
"In this way, we will ensure that U.S. funding is being used to promote shared objectives in the region, including a secure and stable Egypt and the defeat of terrorist organizations," said National Security Council spokeswoman Bernadette Meehan. "These measures put our assistance programs more in line with current core U.S. priorities."
The Obama administration suspended its assistance to Egypt amid the army's violent crackdown on the Muslim Brotherhood, who rallied in support of ousted President Mohamed Morsy, the Arab nation's first democratically elected leader.
The Obama administration refused to label the incident a coup, which would have required cutting all humanitarian aid.
The 2013 decision to end military aid was a compromise move that allowed the U.S. government to maintain its relationship with Cairo while still exacting a price for the crackdown.
Aside from the delayed delivery of the F-16s, missiles and tanks, the United States halted a $260 million cash transfer to Egypt. Officials said at the time that some of the aid would be "repurposed" for humanitarian concerns.
Photos: Deadly violence on anniversary of Egypt revolution
A man carries activist Shaimaa El-Sabbagh after she was shot near Tahrir Square during the protests on Saturday, January 24. Protests marking the anniversary of the 2011 uprising that toppled Egyptian President Hosni Mubarak have turned deadly. The death of Cairo protester Shaimaa El-Sabbagh was captured on video. More than a dozen others have been killed.
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Photos: Deadly violence on anniversary of Egypt revolution
Egyptian security forces deploy in the Cairo suburb of Matariyah on Sunday, January 25. Egypt tightened security in Cairo and other cities Sunday as police moved to break up scattered protests marking the anniversary of the 2011 uprising that toppled Hosni Mubarak.
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Photos: Deadly violence on anniversary of Egypt revolution
Opponents of Egyptian President Abdel Fattah el-Sisi run for cover during clashes with pro-government demonstrators on January 25 in Cairo.
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Photos: Deadly violence on anniversary of Egypt revolution
Smoke rises as a car burns in Cairo on January 25.
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An injured protester is carried during the protests on January 25.
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Photos: Deadly violence on anniversary of Egypt revolution
A taxi burns during clashes in the Cairo suburb of Matariyah on January 25.
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Photos: Deadly violence on anniversary of Egypt revolution
Protesters burn tires in Matariyah on January 25.
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Photos: Deadly violence on anniversary of Egypt revolution
Egyptians march in the funeral procession of Shaimaa El-Sabbagh in Alexandria, Egypt, on January 25. El-Sabbagh was shot Saturday in downtown Cairo while taking part in a gathering commemorating protesters killed in the revolution.
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The coffin of Shaimaa El-Sabbagh is carried out of the Zenhom morgue in Cairo early on January 25.
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The move was meant to be reversible. Officials said military assistance to Egypt would resume if the country's new government took steps toward restoring democratic rule, and Congress passed legislation requiring the administration to verify those steps were being taken before releasing the stalled aid.
Since then, human rights groups have reported that thousands of opposition political activists have been jailed, along with journalists who were accused of airing reports sympathetic to the Muslim Brotherhood.
The White House said Tuesday it "will not make the so-called 'democracy certification'" in this year's allotment of military aid to Egypt, but did say Obama raised human rights issues in his phone call with el-Sisi.
Obama "reiterated U.S. concerns about Egypt's continued imprisonment of non-violent activists and mass trials" and "encouraged increased respect for freedom of speech and assembly," the White House said in its description of the call.
Meehan said the White House "will continue to engage with Egypt frankly and directly on its political trajectory and to raise human rights and political reform issues at the highest levels."
