She set out plans for a crackdown on illegal activity, which could see land managers and owners facing up to six months in jail if their workers - for example gamekeepers - are caught poisoning the protected species.
Four golden eagles were among the 16 birds of prey poisoned in the first half of this year. There were 28 incidents during the whole of 2009.
Ms Cunningham warned that employers would no longer be able to "turn a blind eye" to such incidents under proposals to update wildlife protection laws.
The minister told MSPs yesterday: "A year ago I wanted to be able to stand here telling parliament that the persecution of birds of prey had become a rarity and that poisoning statistics had shown a marked decline.
"Sadly, I cannot do that. I cannot do that because 2010 is set to be one of the worst years on record for poisoning of birds."
The government is now to introduce an amendment to the new legislation that could see countryside employers hit with tougher punishments if their staff poison birds of prey.
As well as jail sentences of up to six months, the "vicarious liability" offence would mean that employers could face a fine of up to 5,000.
There will be a defence of due diligence by bosses.
MSPs yesterday backed the general principles of the Wildlife and Natural Environment Bill.
Earlier this year, the Scottish Government published a map showing poisoning "hotspots" across Scotland between 2005 and 2009.
There were 23 incidents in the Highlands and Islands, the highest in Scotland, with 20 in Lothian and Borders.
Of the 16 birds of prey poisoned in the first half of this year, there were three buzzards, five red kites, four golden eagles, two peregrine falcons, one sparrowhawk and one sea eagle, according to Science and Advice for Scottish Agriculture. The government agency reported a 30 per cent increase in all types of submissions to the lab for testing.
A rare prosecution last month saw a gamekeeper on the Hopetoun Estate in South Lanarkshire fined 800 after pleading guilty to planting a poisoned rabbit carcass on a country estate. Lewis Whitham, 20, was caught by a researcher from Advocates for Animals.
A stream of high-profile poisoning incidents in Scotland have sparked anger among conservationists and campaign groups.
In May, three golden eagles were found dead in Sutherland, the victims of a suspected poisoning.Their deaths, and those of two other birds of prey, are being investigated.
A golden eagle found dead in Argyll in June 2009 had been poisoned with insecticide.
And there was worldwide condemnation in August 2007 after a ten-year-old female bird, one of a breeding pair, was killed in Peeblesshire.