Medics at Hillingdon Hospital and Mount Vernon Hospital, both in Middlesex, discovered the grim traces while preparing for surgery this week.
The contamination was discovered initially at Hillingdon Hospital on Wednesday, with operations continuing with clean instruments checked by theatre staff.
Altogether about 200 kits that were supposed to have been cleaned, were provided to the hospitals by IH Sterile Services but 24 were found to be contaminated.
The hospitals, run by Hillingdon NHS Trust, suspended operations on Thursday afternoon to return all the kits to be checked again.
Officials said that operations has resumed as normal yesterday.
An spokesman for IHSS said: "We are dismayed that one of our new, high-tech decontamination units, operated by experienced personnel, has failed in this way.
"We have begun an urgent investigation to establish the cause of this clearly unacceptable situation.
"We are determined to correct matters and are placing additional safeguards at all our facilities, with additional inspection requirements.
"We apologise wholeheartedly to the patients and hospitals we have inconvenienced."
IH Sterile Services provides sterilisation to numerous hospitals across England.
The dirty instruments had been delivered from a centre in Ruislip.
A trust spokesman said: "We are waiting for the full results of the inquiry and they are working very hard to give us answers to the questions.
"They are normally a reliable company.
"This seems to be a one-off aberration."