Dennis Canavan, one of two MPs who are fighting the decisions, said a "partial ideological cull" had taken place, with left-wingers and troublemakers excluded from the list.
Left wing Labour MPs with English constituencies said last night that they feared a cull of troublemakers south of the border.
"We are likely to be asked whether we have ever said anything to embarrass a minister. It was the McArthyite question that was put to Dennis Canvan. At least he had the guts to say it was his duty to ask awkward and embarrassing questions," said one prominent left-winger.
"The whips are claiming we have a bad voting record. Then they will get us deselected," said the MP. The MPs fear that they will be replaced with Blairite members, who came into the Commons in 1997 in marginal seats. Already a handful are reporting interest in their seats by neighbouring colleagues.
The move against Mr Canavan came after whips at Westminster supplied a list of 11 occasions when he abstained or voted against the Government since May 1997, and at his interview he was asked if he had ever posed any awkward or embarrassing questions in the House.
Mr Canavan, the MP for Falkirk West, has appealed along with Ian Davidson, MP for Glasgow Pollock. The number of appeals before yesterday's deadline was likely to rise to around 20, he said.
While Mr Canavan and Mr Davidson were rejected, other left-wingers including John McAllion, the MP for Dundee East, were accepted. Donald Dewar's special adviser, Murray Elder, was rejected along with Mark Lazarowicz, a former Edinburgh council leader, and Esther Robertson, former co-ordinator of the Scottish Constitutional Convention.
Mr Canavan's letter of appeal said the chair of the selections board, Rosemary McKenna, MP for Cumbernauld and Kilsyth, had an interest in the process because her daughter was a successful applicant. As Mr Canavan's constituency was next to Mrs McKenna's, Suzanne McLeod might be expected to seek selection for Falkirk West if she failed to win a seat in Cumbernauld and Kilsyth, he said.
"Mrs McKenna should not have been even a member of the selections board," he said.
He also claimed other potential nominees were coached before his interview, while he was not offered any training. Leaked media reports had predicted that he was to fail in his bid before the selection board made its decision, he added Even before his interview, senior party figures were trying to discredit him. Mr Canavan's interview was chaired by Ernie Ross, MP for Dundee West, with whom "I do not see eye to eye, and that is an understatement".
Scottish Labour released a "person specification" drawn up for the ideal candidate, which said he or she must show creative skill, strategic thinking, advocacy and interpersonal skills, leadership, teamwork, communication and the ability to campaign effectively.
Candidates must also have useful experience within and outside the Labour Party, must be committed to and knowledgeable about the Scottish Parliament and to equal opportunities.
Of 534 applicants, 167 were allowed to go forward after the interview process. They must now apply to constituencies, which are "paired" and must choose a man and a woman between them to achieve a gender balance.
Party officials suggested that the appellants were happy to vote the selection process through at the Scottish Labour conference this year, and had only complained about it after they were rejected.
Alex Rowley, the Scottish Labour Party's new General-Secretary, said: "The party approved the process for selecting the candidates for the Scottish Parliament and believe it was a fair process.