"There was a reduction in payments to BT due to some availability issues with the spine. This is some £300,000 - 30% of the initial payment of £900,000," the NPfIT said.
"The spine issues have not had a fundamental impact on implementation plans."
In June, Computer Weekly reported that BT faced a six-figure fine for failing to meet two of its 56 milestone "deliverables" under a £530m, seven-year contract to deploy an N3 broadband infrastructure across the NHS, and that it had missed interim targets to deliver the national data spine.
None of the national programme's other national application service providers or local service providers have had payments withheld in this way, an NPfIT spokesman told Computer Weekly.