Maroš Šefčovič said "political will" is needed as he once again outlined EU proposals to cut checks.
The remarks come as a Department for the Economy report suggests that the protocol creates a mixed picture for attracting manufacturing investment.
The protocol gives Northern Ireland manufacturers unique access to the UK market and the EU single market.
Mr Šefčovič's comments are being downplayed by some in Brussels after technical talks resumed just over a month ago.
His remarks appear to be largely based on hopes that the UK could sign up the EU plans for easing controls on good travelling from Great Britain to Northern Ireland to as little as "a couple of lorries" per day.
Mr Šefčovič was addressing a meeting of MPs and MEPs in Westminster.
"Is it too much to do this?" he asked.
"Cannot we find pragmatic, technical solutions to make these things work?
"I believe that it could be done and if there is political will I am sure that we can sort it out really within a couple of weeks."
He suggested that Brussels needed to be sure that officials at Northern Ireland ports would stop lorries where risk analysis showed certain items, such as "poisoned shrimp" or "dangerous toys", may be on board.
However, goods being sent from Great Britain to Northern Ireland require a range of controls and checks which add cost and complexity.
Last year, the Department for the Economy commissioned the investment consultancy Wavteq to analyse the potential impact of these arrangements.
The department has now published a summary of Wavteq's findings but has not released the full report.
"NI has maintained access to the EU single market for goods and, at the same time, remains in the UK customs union," it found.
"A foreign investor setting up in Northern Ireland can continue to trade with both the EU and UK without additional checks."
The report continued: "However, there are now customs checks on goods travelling from GB to NI and it is a key source for NI supply chains.
"The overall impact of our new trading relationships may be more positive for foreign investors seeking access to both the GB and EU markets with less regulatory obstacles to trade in goods.
"The overall impact may be less positive for NI based companies dependent on GB supply chains."
It adds that individual investors will need to weigh up "complex decisions" about how and where to invest.
Separately the UK's Europe minister has said the government is neither "expediting" or "halting" the Northern Ireland Protocol Bill.
Leo Docherty told the same meeting of British and European politicians: "We're just letting it go forward."
The bill was introduced under Boris Johnson's premiership and initially driven forward by Liz Truss.