Ofgem said that while firms across the sector had met 99% of energy efficiency goals by the year-end deadline, it would be looking into those that failed one or more targets.
Suppliers British Gas, SSE, Scottish Power, as well as generators Drax, GDF Suez / IPM and Intergen, are now facing investigations by the regulator.
The targets were set under two schemes launched by the Department of Energy and Climate Change in 2008 to get energy firms to reduce emissions and also to help the most vulnerable customers by insulating homes and replacing boilers to improve efficiency and save money on their bills.
Suppliers and generators were asked to deliver the energy saving measures to consumers, with £54 added to annual household bills to pay for the schemes.
Ofgem said since then, more than 3.9 million lofts and 2.5 million cavity walls had been insulated, while 150,000 vulnerable households received at least one energy efficiency measure.
Ofgem revealed that suppliers EDF Energy, E.ON, RWE npower and independent generator Eggborough power achieved all of their energy efficiency targets.
But of those that are being investigated, British Gas was found to have met less than two thirds - 62.4% - of its targets under the Consumer Energy Saving Programme (CESP), while Scottish Power met 70% and GDF Suez/IPM and Intergen hit only 38.6% and 6.5% respectively. SSE, which was recently fined £10.5 million for mis-selling, achieved 90.9% of the CESP target.
Energy and Climate Change Secretary Ed Davey said: "I am disappointed that under the old schemes, some companies failed to meet their obligations. Ofgem will be conducting a thorough investigation and will take any necessary enforcement action. We are already acting through the Energy Bill to give Ofgem the teeth it needs in future to get compensation to those directly affected."