"The accident occurred at 09.55 Moscow time [05.55 GMT] on Sunday at the Dzemgi airfield during the Su-35 prototype's take-off," Vitaly Tyulkin said, adding that the pilot ejected safely.
"We will announce the details of the accident later in the day," he said.
Sources earlier said the accident could have been caused by a faulty fuel pump.
The aircraft was one of the three prototypes to test the new fighter, which has been billed as "4++ generation using fifth-generation technology."
The Sukhoi aircraft maker said in March that successful flight tests involving two prototypes had confirmed the earlier-announced timeframe for deliveries of the aircraft to Russian and foreign customers in 2011.
The company had planned to add a third prototype to the testing program in the second half of 2009, and to boost the current number of test flights to 150-160.
Su-35 fighter, powered by two 117S engines with thrust vectoring, combines high maneuverability and the capability to effectively engage several air targets simultaneously using both guided and unguided missiles and weapon systems.
The aircraft also features the new Irbis-E radar with a phased antenna array, which allows the pilot to detect and track up to 30 air targets, while simultaneously engaging up to eight targets.
It is equipped with a 30-mm cannon with 150 rounds, and can carry up to eight metric tons of combat payload on 12 external mounts.
Sukhoi plans to export at least 160 Su-35 fighters to several countries including India, Malaysia and Algeria.