Cruise Scotland raised the issue with the convener of Holyrood's cross-party group on marine tourism, Stuart McMillan, who has complained on its behalf to the Home Office.
In the past, the UK Border Force (UKBF) has cleared cruise ships on the basis of passenger and crew manifests submitted in advance, but this has been changed with little consultation to a system whereby all passengers must undergo a full face-to-document check on arrival at the first UK port of call.
Cruise Scotland chairman Richard Alexander wrote: "Scotland receives a large volume of transit calls arriving from foreign ports in comparison to the rest of the UK.
"A number of cruise lines have already expressed extreme dissatisfaction over the current UKBF stance on completing face-to-document checks and passing on additional unwelcome costs.
"At a time when cruise lines are already facing increasing operational costs, this is effectively a new tax on their operations. They have also indicated this will make the UK uncompetitive and unappealing and act as a deterrent for ships to call at UK ports."
Some ships can have up to 3600 passengers and 1200 crew, and critics of the new checks say they could lead to significant new bureaucracy, with the costs passed on to the sector.
Cruise ship visits generated an estimated £41.2 million for the Scottish economy in 2012 and almost 40% of tourism from cruise ships into the UK arrives in Scotland. Passenger numbers swelled from 45,000 in 2000 to 240,000 in 2010.
According to statistics from Cruise Scotland, a membership-based organisation that promotes Scottish ports within the industry, this represents 436 cruise calls and 379,955 passengers – an increase of 14% and 19% respectively on 2011. A study commissioned by Cruise Scotland suggests that, with investment, visitor numbers could reach 1.1 million by 2029.
Testament to the country's soaring popularity in the sector, Cruise Scotland was awarded Destination of the Year at the Seatrade Cruise Insider Awards 2012 in Marseille, France, last month.
Mr McMillan, SNP MSP for West of Scotland, has written to Immigration Minister Mark Harper expressing serious concerns about the new immigration checks for cruise ships.
He said he had sought "clarity on how these rules are affecting Scotland, as the voices from the industry say it is hugely negative and must be changed before it is too late".
In his letter to Mr Harper, he writes: "I am led to believe no advance warning or consultation has taken place with ports over the changes. Also, there are apparent inconsistencies in implementing the checks on a UK-wide basis."
He requested details of the new proposals and wanted to know how they will affect Scotland.
A UKBF spokesman denied industry claims that the procedures have been changed or tightened up, insisting: "There have been no changes to immigration rules affecting cruise ships. We conduct full checks on all cruise passengers entering the UK to ensure our borders are not compromised.
"We welcome genuine visitors to the UK and we are in discussions with Cruise Scotland to make sure effective plans are in place to protect the border with the minimum inconvenience to passengers.
l Scotland is the UK market leader for inbound cruise tourism, attracting around 38% of all calls and 59 of the 101 vessels operating on the Northern European circuit.
l Popular itineraries from Scottish ports include round-Britain and Ireland cruises as well as to Iceland, the Faroe Islands and the Norwegian fjords.
l Most visitors are from North America (44.9%), followed by the UK (35.5%) and Germany (17.1%).
l Among the most frequent cruise line ships calling in Scotland are Princess Cruises, Fred Olsen Cruise Lines and Aida Cruises, part of Carnival Group.
l There are 15 main cruise ship ports of call: Aberdeen, Edinburgh, Fort William, Greenock, Holy Loch, Invergordon, Inverness, Lerwick, Oban, Orkney, Peterhead, Portree, Scrabster, Stornoway and Ullapool.
l The busiest is Orkney with 77 calls and some 41,500 cruise passengers arriving into Kirkwall and Hatston during 2012.
l Edinburgh came a close second with 76 ship visits and 79,800 passengers through Leith, Rosyth and South Queensferry combined last year. Invergordon proved popular too with 67 calls and 77,100 passengers arriving in the Highland port.
l Greenock expects record numbers for 2013 with an expected 83,000 passengers and 40 ships. Last year saw 66,300 passengers.
l Ships making their maiden calls to Greenock this year include Infinity, Mein Schiff I, Eurodam and MSC Magnifica. The busiest period will come during May when five ships will be calling within six days.
l Cruise lines visiting the Clyde this year will include Carnival, Princess, MSC, Holland America, Celebrity, Cunard, Royal Caribbean International, Saga and Fred Olsen. At 150,000-tonnes Cunard's colossal Queen Mary 2, arriving in Greenock on May 15, is the largest ship, although Caribbean Princess and Emerald Princess carry the most passengers, around 3600 apiece.