Nemtsov told Ekho Moskvy radio that he suspected that Kremlin-backed Nashi activists carried out the attack in response to his criticism of Russia's plans for the 2014 Winter Olympics in Sochi.
A Kremlin spokesman declined to comment on the allegation. Phone calls to Nashi went unanswered.
The incident coincided with the publication of an open letter to President Dmitry Medvedev in which Nemtsov said preparations for the Olympics would strain Sochi to the breaking point and suggested that many events be held elsewhere in Russia.
Nemtsov was attacked outside his campaign headquarters in Sochi, spokeswoman Olga Shorina said by telephone. She said a person with long hair, women's clothes and a deep voice approached him with a bouquet of flowers while an assailant splashed him with ammonia.
Some got in his eyes, but he apparently suffered no lasting injury and went ahead with a scheduled news conference after a delay, Shorina said.
Police were called immediately, but more than an hour later they had yet to arrive, she said.
RIA-Novosti later cited an unidentified police official as saying investigators had taken fingerprints from the bottle and were using security-camera footage in an attempt to identify the assailants.
Nemtsov linked the attack to his letter, which was published Monday in Novaya Gazeta, and to a critical report he said he and others are compiling that would "reveal the truth" about the Olympic preparations.
"Naturally, this is not very pleasant for the government, and they are fighting against us with their criminal methods," he told Ekho Moskvy.
The International Olympic Committee awarded the 2014 games to Sochi after an impassioned address by then-President Vladimir Putin, who personally backed the bid. Holding the games will require major upgrades to roads and other infrastructure, and the venues for ice sports must be built from scratch.
In his letter to Medvedev, Nemtsov said Sochi cannot handle the games without major improvements that would cost even more than current plans and that construction for the games will cause irreversible environmental damage and drive people from their homes.
The attack came hours before Medvedev and Putin met with federal and regional officials in Sochi. Neither leader mentioned the incident in televised comments from the meeting, but Putin -- in a remark about the election that seemed aimed at Nemtsov -- said that "politicians should not use the Olympics to further their own goals."
Putin also said the new mayor would have to build relations between Moscow and local officials.
A Message from The Moscow Times:
Dear readers,
We are facing unprecedented challenges. Russia's Prosecutor General's Office has designated The Moscow Times as an "undesirable" organization, criminalizing our work and putting our staff at risk of prosecution. This follows our earlier unjust labeling as a "foreign agent."
These actions are direct attempts to silence independent journalism in Russia. The authorities claim our work "discredits the decisions of the Russian leadership." We see things differently: we strive to provide accurate, unbiased reporting on Russia.
We, the journalists of The Moscow Times, refuse to be silenced. But to continue our work, we need your help.
Your support, no matter how small, makes a world of difference. If you can, please support us monthly starting from just $2. It's quick to set up, and every contribution makes a significant impact.
By supporting The Moscow Times, you're defending open, independent journalism in the face of repression. Thank you for standing with us.
Remind me later.