Rahesabz.net said that mourners shouted slogans in support of the opposition Green movement and that police fired tear gas and beat protesters.
The Jaras website reported that "police fired teargas to disperse people ... many people were injured ... some arrested".
Reporting restrictions in Iran make such incidents impossible to verify.
Alireza Ronaghi, Al Jazeera's correspondent in Iran, said witnesses told him they had not heard any shots fired.
Parlemannews, the website of Iran's reformist minority faction in parliament, said that "over 50 people, including four reporters, were arrested in clashes".
A second demonstration was also reported to have taken place near Isfahan's Sayed mosque, this one in support of the government.
Mehrdad Khonsari, a former Iranian diplomat under the Shah and currently an Iranian affairs analyst in London, said the reported protests indicate an "incremental increase in pressure" on the government.
"Having sidelined Ayatollah Montazeri, [the government] cannot allow for great celebrations of his life to be carried out given the fact that, that would be counter to the kind of policies they have been making in the course of the last 20 years," Khansari told Al Jazeera.
"So the opposition is incrementally increasing the pressure and the government has no choice but to try to stand against them and the result is what you see.
"You see more vocal protests and more people becoming disenchanted and one riot and protest leading to another."
Al Jazeera also received reports on Wednesday that the home of Ayatollah Seyed Jalaleddin Taheri had been surrounded by pro-government forces.
Taheri was among the religious leaders who had denounced the June re-election of President Mahmoud Ahmadinejad as illegitimate.
In yet another political development, Mir Hossein Mousavi, the main Iranian opposition leader who went head to head with Ahmadinejad in the disputed election, has been sacked from his government post.
Mousavi was dismissed as the president of Iran's Academy of Art - a post he has held since its inception in 1999.
Ahmadinejad heads the council that sacked Mousavi.