The International Convention for the Regulation of Whaling (1946) is the legal agreement which establishes the International Whaling Commission. Article VIII of the Convention states that countries are permitted to kill whales for scientific research purposes. Article VIII gives responsibility for setting and regulating these catches to individual governments, not the IWC.
Although the IWC does not regulate special permit whaling, Article VIII does stipulate that any country undertaking special permit whaling should report to the IWC each time a permit is issued. It also states that the scientific information produced by the special permit whaling should be presented, at least annually, to the Commission. This information is received by the IWC Scientific Committee which reviews all special permit whaling proposals and the results of any programmes (see below) using a process known as 'Annex P,' . The Scientific Committee's findings are reported to the Commission.
The Commission often makes comments on proposals it receives from Contracting Governments to establish or modify special permit programmes. It does this by passing Resolutions. These Resolutions are not legally binding and the government conducting the special permit whaling programme are not obliged to act on the comments of the Commission.
It is well documented that IWC member governments have been unable to reach agreement on special permit whaling. In 2010, the Government of Australia (with New Zealand intervening) brought a case against the Government of Japan at the International Court of Justice regarding Japan’s Special Permit programme in the Antarctic (known as JARPA II). In March 2014 the court delivered its Judgement. You can read the Judgement and related papers here.
As a result of the Judgement, the Government of Japan ended the JARPA II programme. The implications of the Judgement were discussed at the IWC Commission meeting in September 2014. Consensus could not be reached but a Resolution was adopted by vote. You can read a report of the discussion in the Chair’s Report of the Meeting here. You can read the Resolution (2014-5) here.