As a reward for information about the deaths of the birds reached £26,000, Paul Wheelhouse spoke of his "anger, revulsion and utter frustration" that crimes such as the killing of 16 red kites and six buzzards in Ross-shire still occur.
But Mr Wheelhouse said it is now likely that 100 red kites had been killed in Scotland in the last 25 years.
He said: "The death of so many birds in a single incident is very likely to have a significant impact on the population in an area where huge efforts have been made to reintroduce them.
"Many of these kites were established breeding birds which would have contributed to the population. However, this incident is only part of the story. The red kite population in this area was reintroduced at the same time as a similar number of red kites were released in the Chilterns in England.
"Now, though, there are roughly six times as many birds there as in the north of Scotland.
"While there may be other factors, the difference is most likely, if not entirely, due to illegal killing here in Scotland."
Mr Wheelhouse added: "I regret that if toxicology confirms the suspected poisonings we have probably now passed a shameful landmark
"And that is the recording of 100 illegally killed red kites in Scotland since 1989."
He insisted: "Let me be absolutely clear - the Scottish Government is determined to stamp out this deeply unpleasant and pernicious criminal behaviour. If and when we judge it necessary I am prepared to take further action.
"We are implementing measures I believe will have an impact, but our patience and that of Parliament is not infinite.
" This Government and I believe this Parliament are determined to rid Scotland of a blight on her reputation."
Mr Wheelhouse was speaking during a Holyrood debate on wildlife crime. He agreed to a call from Labour for the Scottish Government to carry out a review of licensing and game bird legislation in other countries.