In a report on the proposed changes to S4C's funding and governance, following last year's comprehensive spending review, the committee called on the government to ensure the channel's editorial and managerial independence "is not compromised".
It also asked for more detail on S4C's future funding and governance. Under the proposed arrangements, S4C's funding will move from a direct Department for Culture, Media and Sport grant to funding through the BBC licence fee.
"We welcome the commitment made by the DCMS and the BBC that S4C's editorial and operational independence will be maintained under any new partnership arrangement between the organisations.
"However, we have concerns about how this will work in practice. We call on the government to spell out exactly how this independence will be guaranteed under the new arrangements."
The committee also raised concerns about the BBC's interests in Welsh language programming as a primary focus.
"We note the possibility that under any new structure, S4C's distinctive voice will go unheard. We call on the government and BBC to guarantee publicly that S4C remains solely a Welsh language broadcaster."
This echoed concerns raised by the Writers' Guild in March at a public meeting in Westminster as part of its efforts to lobby parliament to remove S4C from the public bodies bill, which in its current form would give ministers power to modify its funding arrangements.
The committee today called on the government to confirm the funding of S4C beyond 2014/15 "as soon as possible".
"Without this certainty, S4C will not reasonably be able to develop its future strategy. Therefore, we believe that it is essential that there is a long term funding formula enacted in primary legislation."
But the committee added that overall the proposed deal should result in synergies and cost savings for both broadcasters.
"Going forward, we are determined that S4C maintain its central position in the Welsh economy, commissioning more quality and popular programming from Welsh independent production companies, providing only Welsh language services and reaching a greater share of the approximately 600,000 Welsh speakers in the United Kingdom," chair of the committee David T.C. Davies MP said in a release.
"In this new phase for S4C we want to see an increased focus on efficiency and improved audience figures for S4C's output. We note that S4C itself recognises that it must raise its game in these areas."
S4C today said it welcomes the report, which it said would be helpful to S4C "as it maps out its future".
"We are aware that there is work to do in some areas and much of this work has been in hand for some months," Rheon Tomos, chair of the S4C Authority, said in a release.
In a statement a spokesperson for the BBC Trust said the BBC has "a long-standing commitment to Welsh language broadcasting" and remains "committed to a creatively independent S4C".
"We are continuing to work through the detail of the new arrangements for S4C as the BBC takes on greater financial responsibility for it from 2013. The Trust is the guardian of the licence fee and will have oversight of how this money is spent."
A DCMS spokesperson said it is considering the report and will respond to the committee "in due course".
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