Al-Jazeera said in a statement Wednesday it was "delighted" by the release of two journalists after they were pardoned by Egypt's President Abdel Fattah El-Sisi.
But the Qatar-based broadcaster said celebrations were muted because of the time Baher Mohamad and Mohamad Fahmy had spent in prison.
"We're delighted for them both and their families," the statement said.
"It is hard to celebrate though as this whole episode should not have happened in the first place.
"They've lost nearly two years of their lives when they were guilty of nothing except journalism."
The pair were freed along with almost 100 other prisoners pardoned by the president.
Within hours of the announcement, the pair had left prison.
They had been sentenced in a retrial in August to three years for fabricating "false" news in support of the Muslim Brotherhood movement, which is outlawed by the Egyptian government.
The retrial was ordered early this year after an appeals court overturned an initial sentence of seven years, saying the prosecution had presented scant evidence.
Their initial arrest came at a time of a crackdown on the Muslim Brotherhood.
At the time, Qatar, which owns Al-Jazeera, had been supportive of the Islamists.
The broadcaster added that it still wanted justice for more of its journalists who were sentenced in absentia by the courts in Egypt.
"The case for seven journalists convicted in absentia continues," the statement said.
"We urge the Egyptian authorities to quash their cases and let them too get on with their lives."