European Athletics' taskforce chair Pierce O'Callaghan said he accepted that some record-breakers would be "collateral damage" under the measures which suggest resetting pre-2005 marks.
The proposal, which was announced by European Athletics on Monday, was immediately condemned by several athletes with Britain's Paula Radcliffe branding it "cowardly".
"Apologies to the athletes, we never intended to damage their reputation and legacy," O'Callaghan told BBC Radio.
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Under the plan, any athlete breaking a record would have to have been drug-tested many times in the lead-up. A sample taken afterwards would have to be available for retesting for 10 years.
European Athletics' ruling council has accepted the project team's recommendations, which it wants to be extended to world records.
Radcliffe faces having her 2003 women's marathon world record of two hours 15 minutes 25 seconds expunged, but O'Callaghan said there was a bigger picture.
"It (The proposal) is intended to give the public belief and credibility in what they are watching in the sport," he said.
European Athletics will forward a report to the International Association of Athletics Federations (IAAF), which will study it at its Council meeting in August.
If the proposal is accepted, current records failing to meet the guidelines would no longer be officially sanctioned although they would remain on the "all-time list".
O'Callaghan said he had spoken to Radcliffe and Britain's triple jump world record holder Jonathan Edwards, another athlete who could be affected because his mark was set in 1995.
The official compared the changes to English football revamping its structure to incorporate the Premier League in 1992 or rugby union's Six Nations emerging out of the Five Nations tournament in 2000.
"We hope people look at it in that vein, rather than stripping great athletes like Paula of their records," he said.
"Unfortunately, Paula ran her records in a golden period that happens to be two years before the technology moved on.
"People should not look at Paula's records and throw them in with doping records - she achieved her performance, as did Jonathan, with 100 percent integrity."
The IAAF has only stored blood and urine samples since 2005. Other world records under threat would include Mike Powell's 1991 long jump mark of 8.95m and Hicham El Guerrouj's 1998 1500m time of 3 minutes 26.00 seconds.
There is no suggestion that any of these athletes took drugs.
Another British athlete, Steve Cram, weighed into the controversy on Tuesday, dismissing the plan as a "PR exercise".
Under the proposals, Cram's 1985 mile and 2000m European records would be removed from the books.
(The story was refiled to correct the final paragraph to say Cram's European records)
(Reporting by Neil Robinson, editing by Ed Osmond)
