Sir Gus O'Donnell, who was the country's top civil servant at the time of the 2010 coalition negotiations, suggested the first past the post voting system would come under intense pressure once the result becomes clear on May 8.
Speaking at an event hosted by University College London's Constitution Unit on Thursday evening, O'Donnell said what the election was "all about is Scotland". On current projections the SNP is expected to see its number of seats jump from six to nearly all of Scotland's 57 constituencies.
O'Donnell said while the SNP could win 55 MPs with just 4% of the national vote, the Greens and Ukip would not get anywhere near that many MPs despite "a lot more people" having voted for them. He said: "That's going to cause quite a legitimacy issue."
He added of opinion polls that showed national vote share. "I kind of despair. What matters for our parliamentary system and who is the government is seats not votes," he said.
O'Donnell said one the outcome of the election in May would be "legitimacy questions about the voting system" and "why is the relationship between votes cast and seats so wildly out of line".
The former cabinet secretary also said a "rather messy" hung parliament result appeared to be on the cards. But speaking about possible coalition negotiations he dismissed Nick Clegg's tenet that the party with the most MPs should have the first right to try and form a government.
"Clegg's law, whoever has got the most number of seats gets first go," O'Donnell said. "There is no such thing as Clegg's law, apart form Nick Clegg saying it's Clegg's law."