The cuts could affect staff in departments such as communications, HR, finance and fundraising.
The move comes only months after Shelter staff went on strike in protest at changes to their terms and conditions.
Adam Sampson, chief executive of Shelter, said: "In common with other charities and voluntary organisations, Shelter is being affected by the downturn of the economy." He described the redundancies as a "limited package".
Alan Scott, regional officer for the trade union Unite, which represents Shelter staff, said competition for contracts meant third sector organisations were fighting each other for scarce resources. "Organisations are robbing Peter to pay Paul," he said. "There are no additional resources and it's having a huge impact on services."
Scott called on voluntary organisations not to make rash decisions in response to the current economic climate. "Even economists don't know what's going to happen tomorrow," he said. "It's important to play the long game".
Thirty-three Shelter staff will face redundancy by the end of the year, with another 10 posts to go when current staff are not replaced.