Clark said Tuesday van Dongen's move threatens her free-enterprise coalition government and makes it easier for NDP Leader Adrian Dix to be elected premier in May 2013.
"He's made a bad decision," Clark said. "What his decision is going to do is make it easier for Adrian Dix to become premier."
She said she and van Dongen have spent their political lives striving to ensure British Columbia is governed by free-enterprise governments, but van Dongen has now decided to abandon that pursuit.
Van Dongen disagreed with Clark as he prepared to take his seat in the legislature for his first time as a member of the Conservatives.
"I think that the vote is already split and what I'm proposing is what I believe is a good solution for British Columbians in terms of a free-enterprise option," he said. "I think that the B.C. Conservative Party can be that option."
Van Dongen said he looks forward to working with Conservative Party Leader John Cummins, an 18-year retired federal MP from suburban Vancouver who was a member of Prime Minister Stephen Harper's minority governments.
Clark, who has spent her first year as premier highlighting job creation and supporting families as her top priorities, signalled Tuesday her main thrust now centres on political survival.
"I'm focused on one thing and that is holding our free enterprise coalition together," she said. "Leadership is about making sure we provide British Columbians with a free-enterprise alternative."
She said her goals are balancing the budget, keeping taxes low, holding the line on spending and creating jobs.
"Our coalition needs to stick together or we are going to end up with an NDP government," Clark said.
Recently, Clark, a life-long federal Liberal, has been attempting to shore up the party's right flank in an effort to prevent the Conservatives from attracting Liberal votes.
She attended a Conservative-style jamboree in Ottawa where she was endorsed by former Reform Party leader Preston Manning and has recruited two Harper aides to Victoria to sharpen her right-wing edge.
Splits among free-enterprise voters in British Columbia have historically catapulted the NDP to election wins.
Former B.C. premiers Gordon Campbell, Bill Bennett and WAC Bennett were able to hold together free-enterprise coalitions, while former NDP premiers Glen Clark and Mike Harcourt rose to power in part due to free-enterprise splits.
Clark's Liberals, who expressed shock over the frankness of van Dongen's resignation announcement, were quick to suggest he was a lone, lost voice and there would be no further defections.
Abbotsford-Mission Liberal Randy Hawes said he won't be joining van Dongen, but said he is considering political retirement and may not run again in the next election.
Hawes said van Dongen's move to the Conservatives hurts the Liberals, but the party will rebound.
"It can't be helpful, can it?" he said. "There's no way it helps, so sure, it hurts, but I mean it's the kind of thing that happens and it's not the first time somebody's crossed the floor."
Health Minister Mike de Jong, whose Abbotsford West riding border's van Dongen's Abbotsford South riding, said the Liberals are working to re-establish themselves under Clark, who was elected Liberal leader last year.
He said he understands that politicians and political parties endure difficult periods, but "you've got to stick it out."
Finance Minister Kevin Falcon said he's not aware of any other Liberals considering jumping ship.
"My sense is there would be no more," he said. "I'm not aware of anyone else thinking along those lines."
Van Dongen's resignation speech said the core values of the Liberals are crumbling and the government is heading for failure. He attacked the leadership of Clark, saying he has been looking for renewal over the past year, but it hasn't arrived.
He said he's been concerned about the government's failure to answer questions about the $6 million paid to cover the legal fees of two former government aides who pleaded guilty in a scandal involving the sale of B.C. Rail.
The four-term MLA also said the Liberals have failed to explain the recent cancellation of a $35-million deal to grant Telus naming rights to BC Place stadium.
Jobs Minister Pat Bell said he provided van Dongen with three briefings about the failed Telus deal and the former Liberal did not appear dismayed with the answers he received.
NDP House Leader John Horgan said van Dongen's decision to join the Conservatives adds new political voices to the legislature.
"What we've seen with Mr. van Dongen's departure is that the free market of political ideas in British Columbia is coming to fruition," he said. "Van Dongen taking his seat as an independent with a Conservative card, I don't have any problem with that."
The current standings in the legislature are 46 Liberals, 34 New Democrats, three independents (including van Dongen), and two vacancies.
Clark called byelections for the two vacant seats for April 19.