People who commit wildlife crimes could be jailed for up to six months.
SDLP Environment Minister Alex Attwood has introduced tough new penalties which for the first time could see serious and persistent offenders handed custodial sentences.
Fines have been doubled with a new maximum £5,000 levy aimed at providing increased protection for plants, birds and animals in the new Wildlife and Natural Environment Act 2011.
Mr Attwood said he hoped the new law would make perpetrators think twice about their actions.
He stated: "There is a clear message - those committing wildlife crimes will be pursued and prosecuted.
"DoE is about making Northern Ireland a better place to live, work and invest in. This act does that. For the first time custodial sentences will be an option for the most serious and persistent offenders.
"This should make people think and think hard about committing wildlife crime. The public has a part to play as well in reporting wildlife crime to the PSNI so that prompt action can be taken against alleged perpetrators.
"The Act will also provide increased protection for a greater range of plants, animals and birds. I am giving enforcement authorities more powers to investigate alleged cases of wildlife crime, coupled with the introduction of new sanctions against those involved in such activity."
Illegally collecting rare birds' eggs, poisoning birds of prey and badger baiting are among the crimes which are likely to attract higher penalties.
David Wilson from the USPCA said: "We would welcome the introduction of these new sentences. It is something we have been campaigning for for some time and we look forward to its proper enforcement.
"Wildlife crime has been a Cinderella crime for a number of years. It is not happening in urban areas, it's happening in the countryside and will require the co-operation of people like farmers to report anything they see.
"Badger digging or badger persecution is one of the most serious wildlife crimes in Northern Ireland and we believe it to be quite widespread and certainly needs to be redressed. This order will go some way to help."
Wild deer, wild birds, badgers, red squirrels and seals were already protected by legislation.
However, the law has also been extended to prevent the death or injury of the basking shark, sea horse, puffin, red kite and cuckoo.
The penalties for offences under the old legislation would have ranged from £1,000 to £5,000, with an average fine of £2,500.
Mr Attwood added: "The Act highlights the important role that the public sector can take in furthering the conservation of biodiversity when undertaking their functions.
"This is a positive approach as Government as a whole is now committed through the biodiversity duty to protect our natural heritage. This action will deliver social and economic benefits, as well as environmental gains."
The new Act states that bird of prey nests such as barn owl, peregrine and red kite are protected from damage throughout the year.
It also requires all public bodies to further the conservation of biodiversity in their work, in line with the Biodiversity Strategy produced by the Government, and gives stronger protection for Areas of Special Scientific Interest (ASSIs) and to protected species.
Reckless damage or disturbance to protected species, including all birds in the breeding season, is also an offence and puts the onus on the perpetrator to show that they took reasonable precautions to avoid damage, such as by doing work at the right time of year.
RSPB senior conservation officer Claire Ferry said: "This part of the new Act is important because it means all Government bodies and councils must remember wildlife in their work.
"The threat of fines and custodial sentences to persistent individual offenders will also help. We hope this will benefit, for example, our declining urban species such as swift, house sparrow and starling, which are often left homeless after construction work damages their nest sites, or our rivers and the species living in them threatened by pollution."