Alex Salmond's government is failing to live up to many of its ambitious promises on climate change and protecting Scotland's natural heritage, a study has concluded.

The report by the Institute for European Environmental Policy (IEEP) said that the Scottish government's efforts to set new standards on climate and protecting sealife and wildlife have been repeatedly undermined by lack of funding, poor implementation and fears of vested economic interests.

It found that Scottish funding for nature conservation by farmers is the second lowest in the European Union, its world-leading climate target is being undermined by weak action on housing and transport, and its ambitions to have the UK's strongest marine protection zones have been diluted to protect the fishing and energy industries.

The study, commissioned by RSPB Scotland, WWF Scotland and the Scottish Wildlife Trust, concludes that Scotland's ministers are sabotaging efforts to be the best in Europe on the environment.

Stuart Housden, director of RSPB Scotland, said the report had recognised the Scottish National party's willingness to be ambitious but found large gaps between its rhetoric and actions.

The study "identifies major difficulties or complete failures in delivery caused by poor decisions, mixed messages or the lack of or misdirection of resources," Housden said. "Sometimes it seems the government has flinched from taking the tough decisions."

The report has been timed to coincide with a heavily funded marketing and public awareness campaign, led by the Scottish government's tourism and conservation agencies, to brand 2013 the "year of natural Scotland".

The three environment groups, Scotland's largest in Scotland, with about 160,000 members, are pressing ministers to address the report's criticisms. Housden said the IEEP analysis had confirmed that "nature is in retreat" in the Scottish countryside, with 82% of flowering species in decline. This was in part because the devolved government in Holyrood had failed to properly fund conservation measures and species protection programmes by farmers in "high nature value" areas.

Simon Milne, chief executive of the Scottish Wildlife Trust, said ministers should seize their chance to set the UK's highest standards on marine conservation, because plans were stalling in England and Wales. "Scotland is in a unique position to build momentum on these islands to kickstart the recovery of the marine environment," he said.

Government policy and funding on curbing CO 2 emissions from homes and roads had "consistently fallen short of what is necessary," said Lang Banks, director of WWF Scotland. Ministers needed to double their funding of home energy efficiency and recycling programmes.

Salmond, the first minister of Scotland, has won global plaudits for the Scottish parliament's goal of cutting the country's CO 2 emissions by 42% by 2020, while his government's new marine protected areas strategy was due to be more ambitious than similar plans for England and Wales.

However, ministers have failed to meet the annual climate targets for two consecutive years. The IEEP concluded that on climate the Scottish government had relied heavily on policies which did not put pressure on voters to change their lifestyles. That weakness made it more likely that it would fail to hit the 2020 target.

The RSPB has been scathing on the marine protection plans, which fail to include Scottish seabird populations, some of the most important and threatened in Europe. The IEEP said ministers had dropped some special sites because of pressure from the fisheries and energy industries, and chosen less valuable places instead.

The report stated: "Political will to pursue environmental priorities embodied in regulation is not always sustained in the face of economic interests."

Ministers retorted that Scotland has been given one of lowest levels of common agricultural policy funding in the EU because of UK government negotiating mistakes, but Paul Wheelhouse, the Scottish climate change and environment minister, acknowledged that more work was needed to properly bolster their rural, marine and climate policies.

He said that farming funding packages needed to be redesigned to support nature conservation. "In some of the sustainability indicators we could do better," he said.

Wheelhouse insisted, however, that the Scottish government was now bolstering its low-carbon transport policies with a new 40-year strategy and denied it had given in to industrial pressures on marine conservation."We work very constructively with the [fishing] industry, but we did confront them with some difficult issues and they responded positively," the minister said.