New travel rules came into force at the beginning of the year that do not guarantee visa-free travel for musicians in the EU.
Sir Elton revealed that last month he met with Brexit minister Lord Frost, his husband David Furnish and Craig Stanley, an agent at the Marshall Arts touring agency, to discuss the issue.
His statement was read out by Mr Stanley in a Digital, Culture, Media and Sport Committee hearing on EU visa arrangements for those in the creative industries.
Sir Elton’s statement said: “Put bluntly, we are currently in grave danger of losing a generation of talent due to the gaping holes in the Government’s trade deal.
“New and emerging artists will be unable to tour Europe freely – an essential part of their education and development – due to the prohibitive costs of visas, carnets and permits.
“However, despite this looming catastrophe, the Government seems unable or unwilling to fix this gaping hole in their trade deal and defaults to blaming the EU rather than finding ways out of this mess.”
He added his objections “aren’t about the impact on me and artists who tour arenas and stadiums”.
“We are lucky enough to have the support staff, finance and infrastructure to cut through the red tape that Lord Frost’s no-deal has created,” he said.
“The gravest of situations is about the damage to the next generation of musicians and emerging artists, whose careers will stall before they’ve even started due to this infuriating blame game.
“If I had faced the financial and logistical obstacles facing young musicians now when I started out, I’d never have had the opportunity to build the foundations of my career and I very much doubt I would be where I am today.”
At the beginning of the committee hearing on Thursday, chair Julian Knight criticised Lord Frost for failing to attend.
Mr Knight said he felt “dismay” over the move, adding it “raised one or two eyebrows” as he had blamed the G7 conference in Cornwall for the cancellation, an event which he said was not “unexpected”.
In a statement he added: “Parliamentary scrutiny in front of Select Committees is of crucial importance in our democratic system and is particularly important when we have a Government with a majority of over 80.
“It is brought into even sharper focus when the Government chooses to appoint members of the House of Lords to Cabinet. Ministers in Cabinet from the Commons have scrutiny due to questions, Urgent Statements and Departmental questions. They are accountable every day. It isn’t acceptable for Lords not to be accountable when they hold high office.”
In January, Sir Elton joined fellow musicians including Roger Waters and Ed Sheeran in signing a letter which criticised the Government’s Brexit deal for not including visa-free travel for musicians.