Many in the crowd expressed anger at Prime Minister Recep Tayyip Erdogan's government. Rocks were being thrown and some people were shouting that Erdogan was a "Murderer!" and a "Thief!"
The protesters faced off against riot police, who had gas masks and water cannons, in front of the ruling NKP party headquarters.
Earlier in the day, women wailed uncontrollably, men knelt sobbing and others just stared in disbelief outside a coal mine in western Turkey as rescue workers removed a steady stream of bodies after an underground explosion and fire killed.
Erdogan postponed a foreign trip and visited the mine in Soma, about 250 kilometres (155 miles) south of Istanbul. The deaths were caused by carbon monoxide poisoning, officials said.
Erdogan said the tragedy would be investigated to its "smallest detail" and "no negligence will be ignored."
He discussed rescue operations with authorities, walked near the entrance of the mine and also comforted two crying women. Earlier, Erdogan declared three days of national mourning, ordering flags to be lowered to half-staff.
Energy Minister Taner Yildiz said 787 people were inside the coal mine in Soma at the time of yesterday's explosion and 363 of them had been rescued. Scores were injured, Yildiz told reporters in Soma, where he was overseeing operations by more than 400 rescuers.
"Regarding the rescue operation, I can say that our hopes are diminishing," Yildiz said before Erdogan's visit.
Erdogan said there were an estimated 120 workers still inside the mine.
"Our hope is that, God willing, they will be brought out. That is what we are waiting for," he said.
Tensions were high as hundreds of relatives and miners stood outside the mine. The crowd shouted at officials, including when Yildiz passed by, and some wailed each time a body was brought up. A heavy police presence was in place around the mine.
Mining accidents are common in Turkey, which is plagued by poor safety conditions. Turkey's worst mining disaster was a 1992 gas explosion that killed 263 workers near the Black Sea port of Zonguldak.
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