Member states will be free to participate in the scheme on a voluntary basis.
It said it had set aside €500m (£440m; $590m) to support the programme, which it said would also bolster return rates, which it said were now "unsatisfactory" at 36%.
The EU's previous resettlement scheme, adopted in July 2015, has resettled some 23,000 refugees among EU member states. The focus should be on people in North Africa and the Horn of Africa, the commission said, mentioning Libya, Egypt, Niger, Sudan, Chad and Ethiopia.
The official urged the European Union and its Member States to continue the relocation programme in an uninterrupted and improved form, adding that the IOM "will continue to implement pre-departure health assessment, orientation and travel assistance".
"This is part of the Commission's efforts to provide viable safe and legal alternatives for those who risk their lives at the hands of criminal smuggling networks", it said. Approximately 29,000 out of the proposed 160,000 refugees were resettled in European countries under the plan.
The proposal involves admitting refugees to European Union countries over the next two years under the bloc's resettlement programme, which was introduced during the migration crisis that hit the continent in 2015.
Resettlement is managed by the office of the United Nations High Commissioner for Refugees (UNHCR), which selects refugees who have a continued need for global protection. "Investing in more legal pathways, both for protection but also for study or work, is therefore essential", said Dimitris Avramopoulos, commissioner for migration, home affairs and citizenship.
The EU previously had in place a more controversial plan, which ended on Wednesday. Select nations retain the legal right to hold border checks for six months for security purposes.
Avramopoulos however said this should be a "last resort", and that keeping the Schengen area open for travel should be a priority.
According to the statement, the countries receiving the largest numbers of asylum seekers so far are Germany, France, the Netherlands, Sweden and Finland.
Germany, Austria, Denmark and Norway have reinstated border checks at certain points in response to migrant arrivals, while France has also done so, citing a persistent terrorist threat, but these controls are due to expire in coming weeks.
The reintroduction of so many checks raised concerns about the collapse of the Schengen zone, seen by many in Europe as a symbol of unity and freedom.