McLaren subsidiary MES (McLaren Electronic Systems) mandatorily supplies electronic control units to every team in F1.
A new unit for 2013, in preparation for the radical new V6 engine rules next year, caused several problems in recent winter testing.
Martin Whitmarsh, the McLaren team principal, told PA Sport he was "distressed" when he heard about Horner's criticism.
"We'll put our hands up if it's a fault that's derived from the hardware or the Bios," he said.
"You can also inflict ECU problems on yourself by how you set it up, but I will look into it.
"I'll be disappointed if it is our fault because in F1, Nascar and Indycar, we've not yet stopped a car, and we're very proud of that record."
Meanwhile, as McLaren grapples with its uncompetitive new MP4-28, Horner admitted his surprise that the British team scrapped the successful 2012 car in favour of a radical design.
"I think McLaren had a very good car last year," he said.
"Arguably for large parts of the season they had the fastest car, so they will know their own reasons why they have chosen to go the route they have."