The dispute is over organisational changes that are designed to align Shelter with government contracting guidelines.
McDonnell conceded that charities were being "forced" in to a contract culture but said that Shelter had dealt with the pressures particularly badly. "Shelter is an example of how not to respond to financial and contract changes," he told Third Sector.
"Contracts, targets and tight financial limits mean that voluntary organisations are having to operate like commercial firms and the ethos of the voluntary sector is being lost," McDonnell added.
The charity has asked staff to sign new contracts stipulating longer working hours and an end to incremental pay increases.
McDonnell, who has put down an early day motion on the issue (Third Sector, 7 May), accused Sampson of intransigence and urged further talks with union members.
A Shelter spokesman confirmed that Sampson had met McDonnell but declined to comment on their discussion.
He added that 22 staff out of 850 were yet to sign new contracts.