The 2.3 percent excise tax on medical-device makers affects companies that manufacture a wide range of items, including stents, artificial knees, and pacemakers. It does not affect over-the-counter items such as contact lenses or hearing aids.
Toomey said the GOP realistically cannot repeal the health law while Democrats hold the White House and Senate.
"What we can and should do," he said, "is repeal the parts of this bill that we can."
Toomey was one of several Republicans calling Wednesday for using the latest budget showdown as an opportunity to eliminate the tax, which he and other lawmakers have long targeted.
His comments came after a procedural vote advanced a House Republican bill that would fund the government only if Obamacare spending is eliminated.
Senate Democrats are ready to strip out the "defunding" plan, but will need some GOP support to overcome a filibuster threat and advance the spending bill needed to keep the government open past Monday.
By insisting on a vote to repeal the tax, Toomey would be trying to stall the bill, a tactic Democrats likened to holding the government hostage and inviting a shutdown.
But in light of broad support for the tax repeal, Toomey said, "What I'm asking for is completely reasonable."
"It would not result in a government shutdown," he told reporters. "If I get an opportunity to have these amendments, I'm going to win."
He cited a nonbinding vote in March when 79 senators, including 33 Democrats, backed a repeal of the tax, though everyone knew at the time the vote was purely symbolic.
Democrats would be the unreasonable ones if they blocked a plan that had such broad backing, Toomey said.
Senate Democratic leaders, though, could neutralize Toomey's plan if they can attract some Republicans to support the funding measure. Then they wouldn't need his support.
They criticized attempts to add strings to a bill needed to keep the government running.
"At this point, any delay or distraction is too much of a risk, putting us closer to a government shutdown," said U.S. Rep. Frank Pallone (D., N.J.), an author of the health-care law.
Obama spokesman Jay Carney said the White House would not accept a repeal of the medical-device tax. He derided Republicans for trying to use a potential shutdown to achieve "what they couldn't achieve when the bill was passing through Congress, what they couldn't achieve at the ballot box, what they couldn't achieve" at the Supreme Court.
Obamacare supporters say the tax is needed to help keep the law from adding to the deficit and is projected to raise $30 billion over 10 years.
Pennsylvania is the fourth-largest producer of medical devices in the country, home to 576 companies that make such devices, Toomey's office said. He has argued that the tax will stifle innovative, growing companies.
In states with large concentrations of device makers, even liberal-leaning lawmakers such as Sens. Elizabeth Warren (D., Mass.) and Al Franken (D., Minn.) have opposed the tax.
The Senate's symbolic March vote to repeal the tax won support from Philadelphia-area Democrats including Sen. Robert Menendez of New Jersey and Sen. Robert P. Casey Jr. of Pennsylvania. Casey was one of several Democratic cosponsors.
A repeal of the tax also has broad backing in the House, including among local lawmakers. House GOP leaders may insist on the repeal in order to fund the government.
Supporters of the tax argue that the device companies will see a major benefit when more people are insured and are able to acquire medical equipment.
Toomey said he still wants Obamacare repealed - "this is a bill that is simply not fixable, it is damaging our economy, it's costing us jobs, it's reducing paychecks" - but he has argued that those like Cruz who want to threaten a shutdown to erase the law are using the wrong tactic.
Many Republicans fear the tactic will backfire, citing the damage done to the GOP in a 1995 shutdown.
Instead, Toomey sees an opportunity to nix a specific, unpopular piece of the law.
"This is not even controversial," he said.