Welsh leader Andrew RT Davies called for a public spending watchdog to review the Communities First programme, which is spending £30m this year.
It was revealed that one project in Merthyr Tydfil spent most of its £1.5m budget over three years on salaries.
Communities Minister Lesley Griffiths defended the spending as "transparent".
The 3Gs Development Trust in Merthyr Tydfil spent nearly £1.3m of its £1.5m budget between 2012-13 and 2014-15 on salaries and £250,000 on "other project costs", according to a response to a Freedom of Information request by the Welsh Conservatives.
Mr Davies told BBC's Sunday Politics Wales programme that staff costs were "disproportionate".
"It does seem... that a huge amount of the money is going into offices and salaries rather than actually getting into the projects themselves," he said.
"There needs to be a greater look at these figures now, whether that be the Auditor General looking at it or whether that be the Welsh government themselves."
A spokesperson for Merthyr Tydfil council defended the trust, which serves Gurnos, Galon Uchaf and Penydarren, saying salary costs included those for staff on the ground such as youth workers, not just administrators.
Over £300m has been spent on Communities First by the Welsh government since it was launched in 2001, including around £30m in 2015-16.
Communities Minister Lesley Griffiths told Sunday Politics Wales that spending on Communities First was "transparent" and she was "comfortable" with the way money was spent.
"It's our flagship tackling poverty programme, has been for many years, it's a very people-intensive programme," she said.
"We've got our Communities First staff working face-to-face, one-to-one with many of the most vulnerable in our communities in some of our most deprived areas.
"There is robust monitoring of the programme - we monitor the outputs, we monitor the outcomes, there's financial audits done.
"You cannot see staff costs [as] independent to the project - it's absolutely integral."
Sunday Politics Wales is on BBC One Wales at 11:00 BST on 14 June.
Money to help the poorest communities in Wales is being spent on "shiny new offices" and staff instead of improving lives, the Conservatives have claimed.