The Birinchi Mai district court in Bishkek on August 20 approved a request by investigators to extend the duration of the detention, which had been initially set until August 26.
Atambaev's lawyer, Zamir Jooshev, said he will appeal the decision.
Atambaev was arrested on August 8 after he surrendered to police following a violent two-day standoff.
The move to detain Atambaev was sparked by his refusal to obey three subpoenas summoning him to the Interior Ministry for questioning.
Kyrgyz authorities had initially said that Atambaev faced five counts of criminally abusing his office during his 2011-17 term.
After the violent standoff, additional charges were filed against Atambaev, including using violence against representatives of the authorities, organizing mass unrest, masterminding a murder attempt, hostage-taking, and illegal use of firearms.
The standoff between security forces and his supporters resulted in one death of a top security officer more than 170 injuries -- 79 of them sustained by law enforcement officers.
The violence underscored a power struggle between Atambaev and his handpicked successor, Sooronbai Jeenbekov, that has raised fears of instability in the Central Asian country.
The Prosecutor-General's Office told reporters on August 16 that Atambaev's wife, Raisa Atambaeva, was also under investigation, without giving any details.
Atambaeva told reporters that day that the probe against her was launched in connection with the case of the ex-chief of the presidential office's department for judicial system reform, Manasbek Arabaev, who was charged with corruption in June.
More about: Kyrgyzstan