The EU’s foreign policy chief, Josep Borrell, said the ultimate objective was for visa waivers to be extended to all members of the Gulf Co-operation Council, which would mean adding Saudi Arabia, Oman and Bahrain.
The European Commission said it would soon start technical discussions with other Gulf countries interested in such a deal to assess whether they meet the necessary criteria.
It said Kuwait and Qatar were approved because there were low risks of illegal migration and "moderate security risks stemming from the region" could be mitigated through security co-operation and checks at the EU's external borders.
No illegal border crossings by Qatari nationals have been reported in the EU since 2015, while the number from Kuwait has dropped to minimal levels and few people are refused entry from either country, a commission document said.
It cited the economic benefit of developing closer ties with the two countries, at a time when Europe is scrambling to buy energy — such as Qatari gas — from any other supplier than Russia.
The proposal put forward by the commission will have to be signed off by the governments of the 27 member states and the European Parliament before it takes effect.
“Our proposal to lift visa requirements for Qatari and Kuwaiti nationals is a first step to make it easier for people from the entire region to travel to the European Union,” said Mr Borrell.
The visa exemption would allow people into the Schengen area for business, leisure or family visits, although it would not grant the right to work in the EU.
But getting a work permit is also supposed to become easier under the wider package unveiled on Wednesday, which would allow online visa applications for the first time.
The so-called “skills and talent” package is meant to address labour shortages and help to integrate Ukrainian refugees fleeing the war with Russia, many of whom arrived in EU members Poland, Hungary and Romania.
Opening up legal pathways to the EU is a longstanding aim of the commission as it tries to reduce illegal migration, with other asylum reforms bogged down for years in negotiations between member states.
The latest proposals include the creation of an EU “talent pool” where prospective migrants can look for opportunities, which will be piloted this year as a way of finding work for Ukrainians.
Another change is that the five-year residency period needed to settle permanently in the EU can be accumulated through stays in several member states, rather than resetting to zero when someone moves within the bloc.
Migrants will be able to apply for a single work and residency permit from outside the EU and be allowed to change employer and spend up to three months unemployed without losing their status.
“While our member states are busy managing the arrival of over five million people from Ukraine, this does not preclude the need to lay the foundations of a sustainable and common approach to labour migration,” said commission vice-president, Margaritis Schinas.
About 60 countries have visa-waiver agreements with the EU, meaning their citizens can visit for any 90 days within a 180-day period without prior approval. They are still checked against national and Schengen databases when they arrive.