The California Republican declined to say how he'd vote on the Republican plan to repeal the law, unveiled earlier this week, but acknowledged that the plan needs fixing.
Asked by a woman attending the meeting in Oceanside, California, how he would vote on the GOP legislation to repeal and replace Obamacare, President Barack Obama's signature health care law, the Republican lawmaker said he couldn't give a definitive answer.
"I understand you're asking for a 'yes' or 'no,'" Issa said.
"The current bill is not in a form that I approve of," he added. "I'm trying to change it, but ultimately the Affordable Care Act has problems that have to be fixed, so my intention is to keep working on the fixes."
Issa was often booed during the meeting with constituents, while protestors chanted and held signs slamming the Trump administration.
When he challenged residents complaining about possible changes to the affordability of health care to be more fiscally responsible, more jeers ensued.
"In return for not having pre-existing conditions not be grounds for refusal or high pay, we're going to have to say to people, 'You've got to continuously be fiscally responsible," Issa said.
"If you're choosing a lifestyle where you're saying, 'I can afford everything except healthcare ... '" he said before the boos drowned him out.
Issa said criticism of the Obamacare replacement plan is rooted in wanting to see significant changes. Lawmakers in the conservative House Freedom Caucus complain that the measure doesn't amount to full repeal and argue that it replaces the law with another entitlement program.
"There are changes in the GOP that we're looking for," Issa told CNN Saturday. "Obviously, I have things I want to see in it including a large pool for the plans that remain."
Since its introduction, the GOP health care overhaul has drawn significant opposition from lawmakers and a range of health care leaders and industry stakeholders, including doctors and major hospital groups.
At a Thursday news conference, House Speaker Paul Ryan set to touting the GOP's plan.
Paul Ryan's TED talk ignores conservative split on GOP health care bill
Ryan took three questions from reporters and ignored those asking how he would bridge the divide in his party about the plan.
The Wisconsin Republican didn't share how much the plan ultimately would cost or how many people would be covered.
While health care was the main topic of Issa's town hall, he was better received when he spoke about his commitment to seeing a special prosecutor investigate any relationship between Russian officials and Trump associates.
"I was the first Republican to call for the attorney general to recuse himself," he said, referring to Jeff Sessions' decision not to involve himself in a federal investigation of the Trump campaign.
Issa said Americans need an investigation that is open and transparent.
"And we need it, as Americans, for half a dozen reasons," he said. "One is, the Russians tried to interfere with our elections. Two, the Russians are not only bad actors, but they live off of chaos that they continue to try to create in our country."