Tory Lord Cormack said big colonies of bats were putting thousands of churches at risk of damage from their droppings and urine.
He denied his Bat Habitats Regulation Bill was "anti-bats" and said something had to be done to protect churches and tackle the hygiene risk.
But the move was opposed by both the Government and the Opposition, with peers warning a balance had to be struck to ensure bats could co-exist with church congregations.
Lord Cormack said bats were amazing creatures and it was right they should be adequately protected.
"But it is right too that churches should be protected from incursions that threaten their condition and very purpose."
Insisting it was a national problem, he cited the example of a church in Lincolnshire which, he said, was not allowed to repair a door because it might block an access route for 900 bats roosting there.
Some churches, Lord Cormack said, were in a "constant battle with bat droppings and urine," with the stench and hygiene risk affecting weddings and funerals as well as other services.
"We need a sense of urgency," he said. "Over this weekend tens of thousands of bats will defecate and urinate in over 6,000 churches."
The Bill would disapply bat protection laws in churches unless there was no "significant adverse impact" and prevent new building without a local bat survey.
Liberal Democrat Lord Redesdale said churches were one of the last sanctuaries for bats after other habitats had been destroyed.
The Bishop of Norwich, the Rt Rev Graham James, said there were places where the bat population outnumbered the church congregation or total number of parishioners.
"It isn't at all funny for congregations in churches where bats do sometimes rule the roost," he said.
Some churches were at the "end of their tether" in trying to tackle the problem, which added considerably to maintenance and restoration costs, the Bishop said.
For Labour, Baroness Jones of Whitchurch said the Bill did not strike the right balance for bats that had been forced to roost in buildings due to the loss of their natural roosting sites.
Environment, Food and Rural Affairs minister Lord Gardiner of Kimble said the Government could not support the Bill either as churches played a vital part in the survival of bats.
Lord Gardiner said bats in some churches did cause distress and damage and this was why ministers were working with Historic England, Natural England and the Heritage Lottery Fund to tackle the problem.
Ultrasound emitting devices to deter bats and excluding bats from certain interior spaces were part of the initiative.
Lord Gardiner said the "blanket prohibition" in the Bill did not take account of the importance of churches to "some of the most vulnerable bat populations" or the steps being taken by the Government to mitigate the problem.
He said it would put the Government in direct contravention of its international commitments and obligations under the Habitats directive.
The Bill was given an unopposed second reading but stands little chance of becoming law without Government support.
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