Abdolmajid Moradzehi, who assists Molavi Abdolhamid, was arrested late on Monday in Zahedan and accused of “manipulating public opinion”, state media outlet Irna reported.
The aide was also accused of communicating with foreign individuals and media outlets and has been taken to an unknown location.
The atmosphere in the flashpoint city is “more inflamed than ever” since his arrest, Iran International reported on Tuesday.
Mr Abdolhamid, a senior cleric of Iran’s Sunni minority, has been outspoken in his criticism of the government since its brutal response to nationwide protests.
He preaches in the Balochistan regional capital of Zahedan, which has suffered the brunt of state violence since the crackdown began on anti-government protesters.
At least 82 were killed in what would later become known as Bloody Friday, when security forces gunned down protesters, bystanders and worshippers following Friday prayers at the Makki mosque, led by Mr Abdolhamid, in September.
It was the worst single incident of violence in the iron-fist response to the protests, in which hundreds of people have been killed and more than 18,000 imprisoned.
The cleric said security forces had shot at people around the mosque, leading to criticism from officials who described his prayer sermons as “provocative”.
He has repeatedly spoken out against Tehran and in support of protesters, who he said are fighting against “discrimination, corruption and lack of freedom” and has gone as far as to call for a referendum.
“If there were no provocative remarks in the sermons, we would have seen peace in Zahedan,” Iran’s deputy interior minister Majid Mirahmadi said in late October when asked about the persistent unrest.
Iran’s Baloch and Kurdish minorities suffer from long-standing persecution, with many of their clerics publicly supporting protesters demonstrating against the government.
Several people have been executed for participating in the popular movement and dozens of others face being hanged.
Consecutive rounds of new sanctions have been imposed on Iran over its treatment of protesters, targeting senior officials, security force leaders and judiciary officials who preside over what are often deemed sham trials of government dissidents.
European states are pushing for the EU to designate the Islamic Revolutionary Guard Corps (IRGC) — at the heart of protest suppression — a terrorist organisation.