The Prime Minister's office distanced itself from the incident, with one official saying that the issue was a "personal matter" for Yerkel.
Abdullah Gul, Turkey's President, cancelled a visit to China to travel to Soma, but he too was on the receiving end of a backlash, with relatives jeering that his visit was interrupting the work of the rescue services.
Gul described the events in Soma as "a huge disaster", adding: "The pain is felt by us all."
Turkey's biggest labour union called a nationwide strike in protest against conditions in the mines, which they say have deteriorated since privatisation was introduced by the Erdogan Government.
Several thousand people demonstrated peacefully in Istanbul, holding banners with slogans including: "It is not an accident, it is not fate, it is murder". Some staged a sit-down protest in front of police lines.
Police fired water cannon to break up a demonstration in Izmir, the nearest large city to Soma, and there were reports of protests in the southern cities of Mersin and Antalya.
About 1000 trades unionists gathered in Ankara to march on the Labour Ministry, some wearing miners' helmets and waving banners showing the image of Che Guevara. Others targeted Erdogan's ruling AK Party, holding banners that read: "The fires of Soma will burn AKP" and "AKP murderers".
The party faced accusations that it had dismissed a parliamentary motion submitted by the opposition Republican People's Party to investigate safety in the Soma mines. A day earlier, Erdogan said mining accidents were "ordinary things", as he reeled off examples from 19th-century Britain, including the collapse of Hartley Pit in 1862.
The remarks revived anger at Erdogan's failure to tackle the poor safety record of the Turkish mining industry. Hostility to the Prime Minister from working-class heartlands added to the list of enemies the long-serving Islamist has accumulated.
Middle-class protests last year were directed against the Government's close links to property developers. Secularists believe the Prime Minister has reintroduced a religious bias that infringes on personal freedom.
Erdogan has made no secret of his desire to become Turkey's first popularly elected President. But the drive to consolidate his position has reinforced fears that he is playing by winner-takes-all rules ill-suited to a democracy. "The incident with this adviser is one of many things coming together that paints a picture of a Turkey that is now clearly a country that is turning illiberal, if not authoritarian," said a former Western diplomat who served in Turkey.
However, Erdogan's party swept local elections in March despite a corruption scandal that forced him to dismiss four government ministers in December and later also implicated him and family members.
He denies corruption, calling the allegations part of a plot to bring down his Government.
Separately, Taner Yildiz, Turkey's Energy Minister, said he would resign if reports that there was a 15-year-old miner among the dead proved true.
He said that the search for survivors had been hampered by a fire that had spread to a conveyor system.
