Tens of thousands of Bolivians have taken to the streets to reproach President Evo Morales over a police crackdown on indigenous protesters.

The marchers decried the perceived betrayal by Bolivia's first Indian president of his prime constituencies: native groups and environmentalists.

"Evo was a very strong symbol for many people. He embodied principles of justice, of human rights. But now these people are disenchanted," said Jim Shultz, an analyst with thinktank the Democracy Centre, which works on Bolivian issues.

Some Bolivians, such as 44-year-old schoolteacher Juana Pinto, said Morales had proved a disappointment. "This government is the worst and it should go because it attacked human beings, the indigenous compatriots who had given it their support, and now it's turned its back on them," said Pinto, who took part in a march that brought central La Paz to a standstill.

The president issued a statement saying the protests had been a "profound wake-up call" for his government following weekend police action that broke up a march by Indians protesting against a proposed highway through their protected Amazon reserve.

"I could never order such violence as has been seen by the Bolivian people," Morales said in a statement released to news media. He asked for forgiveness from the families of the protesters and urged indigenous groups to hold talks with the government.

Bolivia's main labour federation called a 24-hour general strike on Wednesday. It appeared only partially successful – most businesses were open.

Morales championed a new constitution in 2010 that granted Bolivia's 36 indigenous groups an as yet ill-defined autonomy. He promised to protect indigenous people from industry and developers.

But since winning election in December 2005 the president has been forced to weigh development against environmental protection. His "revolution" reached a crossroads last year when he decided to pursue a 190-mile (300km) jungle highway funded by Brazil through the Isiboro-Secure Indigenous Territory National Park, or TIPNIS, in the eastern lowlands state of Beni.

About 1,000 people began a march on La Paz in mid-August from Beni's capital, Trinidad, to protest against the highway they say is an open invitation to loggers and coca-planting settlers and a threat to park inhabitants. That march was broken up on Sunday by riot police who used teargas and truncheons, arresting several hundred marchers but later freeing them under pressure from local people.

Bolivia's defence minister resigned immediately in protest at the crackdown and the interior minister followed, accepting responsibility for police actions. Morales announced on Monday that he was suspending the highway project and would let voters in the affected region decide its fate in a referendum. The original protesters against the highway have promised to resume their own march.