"They didn't explain much. Our lawyers in Egypt are trying to understand the legal grounds," Sanaa said.
She added that her brother had his British passport as well as a recently renewed Egyptian passport.
"I assumed after the renewal of the Egyptian passport that he would be allowed."
Alaa Abdel Fattah's 13-year-old son, Khaled, lives with his mother in Brighton, where he attends a special needs school because he is on the autism spectrum.
Khaled spent a month visiting his father in Cairo following his release from prison, but he has now returned to the UK.
"We're really glad to have [Alaa] back in our lives partially free, but he needs to have freedom of movement to live with his son, reunited with him properly," Ms Seif said.
She added: "Khaled needs his father. My nephew… is very, very comfortable in his school and his set-up in Brighton. We can't change. We can't keep creating instability."
Ms Seif said the UK Foreign, Commonwealth & Development Office had been communicating with her family over the issue, but she called on Prime Minister Sir Keir Starmer's office to also give it their attention.
The FCDO said in a statement: "President Sisi's decision to pardon and release Alaa Abdel Fattah was extremely welcome news and a significant step forward."
"We continue to press for his urgent return to the UK at the highest levels with the Egyptian government so he can be reunited with his family. The case remains a priority issue for the UK government."
On Thursday night, Alaa Abdel Fattah and his mother were given the 2025 Magnitsky Award for "Courage Under Fire". Sanaa had to collect the award on their behalf.
Mr Abdel Fattah rose to prominence during the 2011 uprising in Egypt that forced long-time President Hosni Mubarak to resign.
He spent most of his time in prison after 2014, the year after Sisi led the military's overthrow of Egypt's first democratically elected president, Muslim Brotherhood leader Mohammed Morsi, following anti-government protests.
While in power, Sisi has overseen what human rights groups say is an unprecedented crackdown on dissent that has led to the detention of thousands of people.
In 2015, a court sentenced Mr Abdel Fattah to five years in prison for participating in an unauthorised protest.
In September 2019, only six months after he had been released on probation, he was arrested again and held in pre-trial detention for more than two years.
He was convicted in December 2021 of "spreading false news" for sharing a post about a prisoner dying of torture and handed another five-year sentence following a trial that human rights groups said was grossly unfair.
His 68-year-old mother, Leila, launched a 287-day hunger strike last September 2024 to protest against his imprisonment. She lost more than 40% of her original body weight and was twice admitted to hospital in London.