Managing director Ryan Flaherty described the disruption caused by GB Railfreight as “unacceptable”.
Five trains between Scotland and London were affected overnight on Friday and Sunday. Mr Flaherty said he was urgently seeking reassurances about reliability.
There have been intermittent locomotive problems since a new £150 million Sleeper fleet was launched last April.
However, these had been overshadowed by a litany of faults with the new carriages which have left passengers without water, locked out of toilets and fuming over dirty rooms.
In the worst delay, the “Highlander” service from Aberdeen, Fort William and Inverness arrived in London after 3pm on Saturday – six hours 35 minutes late. The Lowlander service from Edinburgh and Glasgow to London on Sunday night arrived around 1pm, some five hours late, while the Lowlander was more than three hours behind schedule.
Both northbound trains that night were also delayed.
London-bound passenger Roz Wood tweeted: “Was a nightmare. No power, no heat, no flushing toilets. Couldn’t believe it when woke up, freezing, and saw [we] were only 35 miles out of Edinburgh.
“Your staff were brilliant but have been put off the sleeper for life!”
Mr Flaherty said passengers would receive a full refund.
He said: “I are extremely disappointed the Caledonian Sleeper was disrupted by a series of locomotive failures over the weekend.
“The current situation is unacceptable to me and our guests. My team are in urgent talks with operator GB Railfreight to seek clear assurances about future reliability.”
GB Railfreight engineering director Bob Tiller said: “Some of our locomotives used on the service have recently suffered from electrical failures, which has caused significant delays.
“We sincerely apologise for any inconvenience. GB Railfreight is conducting an investigation into the reasons for these problems and how they can be prevented.”