Dzhabrail Makhmudov is accused along with his two brothers, their uncle and an ex-policeman of gunning down Ms Politkovskaya at her Moscow home in 2006, a murder that came to symbolise the risks faced by Kremlin critics under Vladimir Putin, who returned to the presidency last year.
Makhmudov was shot on a Moscow street late on Wednesday and taken to hospital where he underwent surgery, Murad Musayev said. He is conscious but unable to move his left leg, he added.
"We have no hard proof that the attack is linked to the trial but there is reason to think so. We know for sure that the people who really followed and killed Politkovskaya are at large," Mr Musayev said. "It is fully probable that they tried to silence my client."
Makhmudov's brother Rustam is charged with firing the shots that killed Ms Politkovskaya. All five suspects have pleaded not guilty.
Ms Politkovskaya made her name exposing state corruption and human rights violations in Chechenya. Her supporters and colleagues believe that those on trial were merely foot soldiers and that the people who ordered the murder have not been revealed.