The Senate gave grudging approval on Thursday to the key executor of Barack Obama's sweeping new climate change plan, voting to confirm Gina McCarthy as the head of the Environmental Protection Agency.

The 59-40 vote, after a four-month standoff by Republicans, puts McCarthy in direct charge of implementing Obama's strategy of using the agency's powers to reduce greenhouse gas emissions that cause climate change.

The prospect – centred on plans to cut emissions from existing power plants – has brought ferocious protests from Republicans and industry associations, and accusations that Obama and the EPA was waging a "war on coal".

"The EPA will play a pivotal role in the execution and implementation of the president's recently announced climate plan," David Vitter, the Louisiana Republican who led the boycott of McCarthy said in a speech on the Senate floor on Thursday. He called the climate plan "dramatic and draconian".

McCarthy spent the last four years at the EPA, as right-hand woman to then-administrator Lisa Jackson, in charge of clean air and climate policy.

That made McCarthy a target for Republicans who oppose curbs on polluters – despite her 30-year record of working effectively with industry and Democrats as well as Republicans. She worked for Mitt Romney when he was the Massachusetts governor.

"It isn't about her. It's about the fact that they don't like the Environmental Protection Agency," said Democrat Barbara Boxer, who heads the Senate's environment and public works committee.

The standoff on McCarthy's nomination left the agency without an administrator for four months, putting climate rules on hold.

McCarthy's elevation now makes her an even bigger target for Republicans, as Obama bypasses Congress and tasks the EPA with carrying out the work of cutting greenhouse gas emissions.

In the hours before the confirmation vote on Thursday, Republican members of the Senate's environment and public works committee accused McCarthy of serving as Obama's "field general" in the war on coal.

They also accused the agency of over-reaching its authority, and Obama of seeking to exert centralised control over the economy.

"The EPA has been a jobs killer," Vitter said.

Other Republicans on the committee lashed out at Obama for affirming the science underlying climate change. The president in his speech last month offered a summary of recent extreme weather events, such as heat waves, droughts, wildfires and hurricanes.

That was uncalled for, Alabama's Jeff Sessions told the committee – despite 105F measured temperature in Washington DC. "The president has been misleading the public on this subject," the senator said.

Roger Wicker of Mississippi took issue with Obama for saying last month he had run out of patience for "flat earthers" who deny the science underlying climate change.

"At the very least, I think it's time for some tolerance in the public discourse regarding the many scientific viewpoints on climate change," Wicker complained to the hearing. "Respect should be shown."

With her confirmation, McCarthy will now oversee the ambitious work of writing new regulations to reduce emissions from the country's fleet of coal-fired power plants. Obama has said he wants to see the EPA propose the new rules by next June, with final regulations in place by June 2015.

McCarthy during her confirmation hearings last April called climate change the challenge of a generation. "We must take steps to combat climate change," she said at the time. But she added: "I am convinced that those steps can and must be pursued with common sense."

The coming curbs on power plants are at the heart of Obama's renewed pledge to cut America's emissions by 17% from 2005 levels by the end of the decade. Such plants make up about a third of America's greenhouse gas emissions.

McCarthy, 58, a Massachusetts native with a strong local accent, had earned a reputation over the years for being "tough but fair" with industry.

She will need those allies now as the EPA moves ahead on the president's climate plan.

McCarthy did win the support of a handful of Republican senators, including Lamar Alexander of Tennessee, Susan Collins of Maine, Jeff Flake of Arizona, Kelly Ayotte of New Hampshire, and John McCain of Arizona.

However, Joe Manchin, a Democrat from the coal-heavy state of West Virginia, voted against McCarthy and then took to the Senate floor to deliver a speech on coal's important role in US history. "You can't tell the history of America without telling the history of coal," he said. "And you can't plan an energy future for America without planning for coal."