The First Minister said boats would not be allowed to fish in Scottish waters - or even pass through en route to Norwegian grounds - unless an independent Scotland joined the EU on favourable terms.
The warning, issued during a speech in Belgium on Scotland's "enthusiastic and engaged" attitude towards the EU, was immediately condemned by opponents.
Scotland Office minister David Mundell said it would be in breach of international law, while Patricia Ferguson, Scottish Labour's external affairs spokeswoman, warned it would "not go down well" with member states.
The clashes come following the row over the First Minister's praise of Russian president Vladimir Putin.
Addressing academics and students at the College Of Europe in Bruges, Mr Salmond insisted an independent Scotland would join the EU on similar terms to the UK within his 18-month timescale and with "no detriment" to other member states. He called it a "practical, common sense approach".
But, in a warning to the 28 countries that would have to agree, he added: "The alternative - the fishing fleets of 12 countries being denied any access to Scottish waters and, as a consequence, their access to Norwegian waters, which is also dependent on Scottish access - is clearly absurd."
In what was billed as a "charm offensive," the First Minister also used his speech to call for a series of EU reforms to help tackle inequality, prioritise green energy and "restore faith" in the bloc's own policy-making.
Among the changes he wanted to see, he called on the EU to get behind "visionary" plans for a wave power supergrid, which would allow Scotland to export green energy to the Continent.
He also attacked Brussels rules that prevented him requiring firms engaged in public contracts to pay the "living wage".
Mr Salmond argued Scotland's contribution to the EU was "constrained" by being part of the UK and its interests in areas such as fishing not properly represented.
He added: "That is a profound democratic deficit.
"It affects all areas of Scottish life. And because of the rising influence of a virulent strain - not just of Euroscepticism, but of Europhobia - at Westminster, it now poses a real threat to Scotland's place in Europe."
Referring to Prime Minister David Cameron's promise of an in/out referendum on EU membership if the Tories win the next general election, Mr Salmond warned: "Unless we choose to change our circumstances this September, we could be dragged out of the European Union against our will."
Boats from a dozen EU countries fish in Scottish water.
The First Minister has previously warned they would be banned if Scotland failed to join the bloc, citing that as a key reason why member states would agree.
However, this was the first time he has suggested they would be prevented from sailing through Scottish waters.
David Mundell, the Conservative Scotland Office minister said: "It has been a telling day for the First Minister's judgement.
"In the morning, we read about his admiration for Vladimir Putin and by afternoon he was threatening EU members with fishing ground blockades - the very members he would need to unanimously accept a new Scottish state.
"It has not been a masterclass when it comes to his diplomacy skills."
Mr Mundell said foreign fleets took only a "very small proportion" of their catch from Scottish waters and added: "In any accession negotiations, other member states would be more likely to press for improved access to Scottish fishing grounds in the North Sea than to make concessions for Scotland.
"An independent Scotland would also be duty bound under international law to grant free passage to Scottish waters for vessels passing through en route to Norwegian waters."
Labour's Patricia Ferguson said: "His thinly-veiled threats about blockading the rest of Europe from Scottish and even Norwegian waters will not go down well with those he seeks to persuade about Scotland's membership.
"These tactics are hardly about 'constructive engagement' or about being a good neighbour that wants to work in partnership with its neighbours."