Richard Lochhead made the claim as MSPs debated the general principles of the Scottish Government's Marine Bill. He said that one of the measures would aim to protect seals by the creation of a new offence.
Mr Lochhead said: "The bill will put Scotland at the forefront of improving seal protection, creating a new offence of killing or injuring a seal at any time, unless under licence."
Members of Holyrood's rural affairs and environment committee have already called for tougher restrictions on killing the creatures, arguing that a new offence of "intentionally or recklessly harassing seals" should be included in the new law.
However, Mr Lochhead said: "A modern approach to seal protection must not be overly restrictive. I am, therefore, somewhat cautious about the suggestion of including a harassment offence in the bill.
"I appreciate the intent behind the recommendation, but I ask parliament to recognise the difficulties of achieving this without unintended consequences on legitimate activities."
Mr Lochhead also revealed to MSPs that Scotland's powers over its waters are to be extended from its current 12-mile limit off the shore.
But Mr Lochhead said: "I can announce that Scotland will be the competent authority for all Scottish waters right out to 200 nautical miles, with allowances for reserved interests."
Labour's Dr Elaine Murray said her party supported the bill, but it could be "improved and strengthened" by amendments.
An environmental report had warned that Scotland's marine environment was "in real need of recovery", she said.
For the Tories, John Scott said his party welcomed the bill and said the government had genuinely tried to balance competing pressures.
"For too long the sea has been regarded purely as an exploitable asset, and an absolute need exists now to look after our seas more carefully than in the past," he said.
But Liberal Democrat Skye and Inverness West MSP John Farquhar Munro said seal populations were at "very high levels" and were causing "immense difficulty" for fishermen.
He said: "Seals are not the friendly, cuddly mammal many people imagine them to be."