A revolutionary vape ban has cleared a major hurdle, with the sale of e-cigarettes restricted to pharmacies as part of a government crackdown on recreational smoking.

Pharmacists will be able to sell vapes with limited nicotine content over the counter once they have a discussion with a person about health harms and confirm they're over 18.

It's a watered-down version of the federal government's initial proposal to require smokers to get a doctor's script in exchange for the Greens vote to pass the legislation in the Senate.

The amended bill will now need to be ticked off by the government-controlled lower house before it can come into law ahead of the July 1 start date.

The peak pharmacy lobby has criticised the scheme, saying their members should only sell products that have a proven therapeutic benefit but Health Minister Mark Butler and the Greens insist the right balance has been struck.

Pharmacies won't be forced to sell vapes as they are private retailers and the price will be set by the market, Mr Butler said.

They retail under the counter for about $50 to $60 after the government increased border surveillance to stop illegal products flooding the market.

People under 18 will need a prescription to buy a vape and they will only be sold in plain packaging and without flavouring to stop kids being targeted.

The opposition suggested a different model rather than a ban, insisting regulating and taxing vapes would be beneficial and still reduce smoking levels while acknowledging adults could make their own choices.

It would still bring in plain packaging but instead apply an excise and licensing regime for sellers similar to cigarettes, opposition health spokeswoman Anne Ruston announced.

It would also set aside $250 million over four years for a new federal police task force.