The Centre for British Teachers was responsible for quality assurance on the Understanding Connexions course which was supposed to give advisers the skills to encourage 13 to 19-year-olds to remain in education and training.
The not-for-profit company was recently awarded the contract to manage a government scheme for fast-track entrants to teaching.
Earlier this year, CfBT was criticised by the Office for Standards in Education over the quality of its distance-learning courses for teachers.
A spokesperson for the Department for Education and Skills said that the course had been suspended in order to ensure that its content was more appropriate.
He said that CfBT would continue to be involved "in the short-term" but that the Government was looking at other options.
Critics had branded the Understanding Connexions course "mechanical" and said that it did not equip advisers to provide the support needed by disaffected teenagers.
It is the latest problem to hit Connexions which is intended to give advice to young people aged 13-19. The scheme has been criticised for undermining existing youth work and for employing staff without adequate training.
Training for 200 advisers will be deferred until a replacement course begins in the autumn.
The Communication and Youth Workers' Union welcomed the decision. It had repeatedly criticised training for Connexions staff - including the longer diploma course which will continue - and had considered advising members to boycott courses.
"The course was very basic and non-analytical. The Government and Connexions partnerships need to remember that young people don't just need advice, they need a proper support service.
"We want a guarantee that no more unqualified people will be recruited as personal advisers. Advisers need proper skills if they are to help some of the most vulnerable people in our society."
A spokesperson for CfBT refused to comment on the Government's decision.