"Is that policy sensible or even realistic?" he wrote. "In Britain the great majority of people (including many in the ethnic minorities) identify themselves as Christian.
"Will extremism be combated by concentrating on a single faith or will it be better fought by proper attention to all faiths?"
Bishop Nazir-Ali said that countries rooted in Christian values "face a serious ideological challenge from extremists".
"Such a challenge cannot be met by turning our backs on the very resources, spiritual, moral and intellectual, that both make it possible to fight extremism and are the reason for our determination to maintain all that is valuable in British polity, culture and public life," he said.
He urged the Government to counter extremism by supporting faith groups in their civic work.
"The Government should be putting its resources wherever civil society is being strengthened, where people are working for social inclusion, where the needs of the most vulnerable are being met," he said.
"Every faith community deserves recognition if it is engaged with the wider community in these ways."
The Bishop pointed to the "thousands who seek to serve their communities, anonymously and humbly, precisely because of their Christian faith".
"Christian convictions are central to any explanation of why thousands of people volunteer for tasks, with no reward, knowing that they are doing the right thing," he wrote.
Bishop Nazir-Ali added that he was not arguing "for any special privileges for my church" but rather "fairness in acknowledging the contributions of its members and in weighing up its arguments for the common good".
He called for a "proper national debate" on these issues and urged Secretary of State Hazel Blears to "understand, and draw on, the enormous resources she has available for promoting community cohesion: the millions of people who are Christians and endorse and practice Christian values".
