The ministry added that they will also summon the ambassadors of the United Kingdom and Canada later in the day.
Authorities arrested in September Ibrahim Metwally, who is linked to the case involving murdered Italian student Giulio Regeni, as he was about to fly to Geneva for a conference on enforced disappearances.
The lawyer, who has founded the Association for the Families of the Disappeared, was detained at Cairo airport.
"We are concerned at the detention conditions that Ibrahim Metwally... is reportedly enduring, and continue to call for transparency on prison conditions in Egypt," said the statement.
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"We call on the Egyptian authorities to ensure the freedom of civil society and the protection from torture that are enshrined in the Egyptian Constitution," it added.
The foreign ministry said the summons was aimed at expressing "Egypt's strong dissatisfaction with the statement's blatant and unacceptable interference in its internal affairs".
He was also accused of having set up an "illegal" group.
The foreign ministry also denied that "torture" was underway in Egyptian prisons.
Metwally had been in touch with the legal defence team of Regeni's family.
Regeni, a PhD student, went missing in Cairo on January 25, 2015 and his body was found days later bearing torture marks.
Egypt has faced accusations that one of its security services murdered the student who was researching trade unions -- a sensitive topic in the country -- but Cairo denied any such involvement.
The government disputes such allegations.