The trial of the director of the Egyptian Initiative for Personal Rights has been postponed until November so that the court can "examine notes and documents."
Bahgat was called for interrogation in June over charges related to free expression after he tweeted last year that the National Election Authority had overseen fraudulent legislative elections.
Bahgat criticised the former NEC president Ibrahim Lasheen and held him responsible for widespread violations in the parliamentary elections.
It is the third criminal investigation against Bahgat because of his human rights activism and investigative journalism, with authorities having previously accused of "military misdemeanour" after an investigation he carried out into military prosecutions.
He was also accused as part of the NGOs foreign funding case.
The EIPR has said that the indictment is the latest part of an ongoing campaign against the EIPR which has been targeted by authorities because of their defence of human rights.
Last year Egyptian authorities arrested three senior staff members; Mohamed Basheer, Karim Ennarah and Gasser Abdel Razek after they met with foreign diplomats to discuss the human rights crisis in Egypt.
They were later released after widespread international pressure including a call by Hollywood actress Scarlett Johansson to release them, but Bahgat's assets were frozen by a terror court, and he was banned from travelling.
Mohamed, Karim and Gasser were also banned from travel and had their assets frozen.
Former EIPR researcher Patrick George Zaki was arrested in February 2020 after he returned to Egypt for a holiday from Italy where he was studying for his master's.
Zaki has been kept in pretrial detention since his arrest.
The organisation has said in a statement: "This harassment will not deter EIPR from the work it started 19 years ago, and continued to do under successive regimes, in defence of the rights of all Egyptians to dignity, freedom and equity."
Some 60,000 political prisoners languish in Egypt's jails where they are systematically tortured and denied medical care.
Rights groups have criticised the justice system in Egypt where detainees are convicted in flawed trials, including mass hearings where there is no time to outline individual evidence.
Many are tried in military courts despite being common citizens.