Kennedy also asked whether denying corporate religious rights would leave companies with no recourse against a hypothetical mandate to pay for abortions.
The case challenged the act's requirement that employer health plans cover most forms of contraception.
Two private companies claim that the rule violates religious beliefs held by them and their owners. They accept most forms of contraception, but object to drugs and devices that they believe impede the implantation of a fertilized egg, which they liken to inducing an abortion.
While the 2012 case addressed the law's central mechanisms for expanding health coverage, this one was far narrower, though it still holds broad implications for the religious rights of corporations.
The plaintiffs, Conestoga Wood Specialties Corp. of East Earl, Lancaster County, and Hobby Lobby Stores Inc. of Oklahoma City, claim that the contraceptive mandates run afoul of the Constitution's protection of religious freedom and a 1993 law known as the Religious Freedom Restoration Act.
Corporations, they argue, should enjoy the same religious protections as their individual owners.
The more liberal justices, especially the court's three women, were skeptical.
Justice Elena Kagan asked whether employers could go beyond contraception and exclude coverage for vaccines and blood transfusions on religious grounds.
Justice Ruth Bader Ginsburg asked whether covering employees for health care could be considered a religious tenet. And Justice Sonia Sotomayor wondered how a corporation could even exercise a religion.
The more conservative justices were equally dubious of the government's defense of the law.
Justice Samuel Alito worried about the effect of denying religious protection to corporations. He wondered whether the government could close butcher shops that follow religious rules, as he said Denmark had recently done.
When he heard that there was no precedent for giving religious exemptions to corporations, Justice Antonin Scalia responded that there was no precedent for denying them either.
Justice John Roberts, who cast the swing vote in favor of the law in the court's 2012 ruling, may not play that role this time, if his questions were any guide. He repeatedly challenged the government's position that it could require for-profit corporations to provide contraceptive coverage while exempting nonprofit religious organizations.
Much of the questioning addressed the burden that female employees would face if the court let employers deny contraceptive coverage.
Solicitor General Donald Verrilli, who defended the law, saw that burden as a compelling reason for the government to mandate compliance regardless of a company's religious orientation.
Several conservative justices asked whether Congress saw the need to ease that burden as truly compelling when it also built exceptions into the law.
The religious liberty law requires that statutes address a compelling interest if they infringe on religious practices. The health law excludes houses of worship from the mandate, and the government has created an exception for nonprofit religious hospitals and universities.
Several justices wondered whether a similar accommodation could be crafted for for-profit companies.
A broad ruling could significantly expand the First Amendment rights of corporations that the court recognized in its 2010 Citizens United decision. That could strengthen the hand of companies seeking to avoid a range of government requirements.
Still, many observers expect a narrow opinion limited to the circumstances of the contraceptive mandate. Roberts raised the possibility of a ruling that applied only to small, closely held corporations.
Regardless of which way Roberts votes, he could not escape a reminder of his pivotal role in 2012, when he wrote the court's opinion upholding the health-care law's individual mandate as a tax.
On Tuesday, Sotomayor observed that the assessment on the plaintiffs if they fail to offer health coverage is also "called a tax."
To the laughter of the audience, the chief justice replied, "She's right about that."
A decision is expected in June.
Robert Field is a law and public health professor at Drexel University, who leads the Field Clinic blog on Philly.com and Inquirer.com.