The law, which still needs to be approved by Holyrood, will protect nearly 200 sites where seals come ashore to rest, moult and rear their young.
The measure is expected to protect at least half of Scotland’s grey and harbour seals by making it an offence to harass them where they are most vulnerable.
The 194 land sites are on top of an existing network of 15 marine seal conservation areas and 33 others which will be proposed later this summer.
They vary widely and can include rocky islets or shorelines, sandy beaches or sandbanks and occasionally grassy areas on some isolated islands.
The law, part of the Marine (Scotland) Act 2010, does not define what constitutes intentionally or recklessly harassing a seal.
But people separating pups from their mothers, attempting to touch or feed the animals, or causing them to “stampede” into the sea could face charges.
Other activities that could prove threatening include “buzzing” seals in a low-flying aircraft or steering a jet ski, speedboat or kayak too close to a haul-out site.
It is hoped the rules will protect seals from harassment that could prove dangerous, particularly for colonies of mothers and young pups.
Scotland’s environment secretary, Richard Lochhead, said: “Seals are one of Scotland’s most iconic species and that’s why we have introduced a raft of new measures to protect them.”
He added that the land sites had been identified after consultation between Marine Scotland, the Natural Environment
Research Council and the Sea Mammal Research Unit.
“Those engaging in the intentional or reckless harassment of seals in these areas will be committing an offence and if caught will be punished appropriately.”
The protection comes after clashes between marksmen and marine conservationists forced a major salmon producer to call off plans to cull seals at an Aberdeenshire harbour in April.
The following month, campaigners gathered more than 6,000 signatures in a petition calling for the Scottish Government to “stop issuing licences permitting salmon farming and angling interests to shoot and kill seals in Scottish waters”.
Animal welfare campaigners have welcomed the new laws.
“We hope that this will lead to all those who share the environment with marine wildlife, from dog walkers to anglers, fish farmers and salmon netsmen, recognising that seals at rest must be left alone,” said Libby Anderson, policy director at animal protection charity OneKind