"Assessing and reporting major risks does not mean becoming involved in politics; rather it would be political to suppress important judgments," he told a House of Lords committee.
Mr Carney said the vote was the biggest domestic risk to the UK's financial stability.
He added that uncertainty was already hitting the growth outlook.
The referendum takes place on 23 June.
The governor said that while the Bank of England had not made "and will not make" any overall assessment of the economics of the UK's EU membership, assessing the implications were necessary for it to do its job - maintaining monetary and financial stability.
"As with the Scottish Referendum, we will communicate as much as is prudent about those plans in advance of any risk materialising and as comprehensively as possible once risks have dissipated," he added.
The governor also reiterated he saw "signs of growing uncertainty about the UK's macroeconomic outlook related to the referendum".
There is the possibility that a vote to leave the EU would "reinforce existing vulnerabilities" in the UK economy, including a risk around the UK's trade deficit, he added.
"I think it's safe to say that it [the UK current account deficit] is running at a rate around 5%... and that is remarkably high for a large advanced economy... The risk around the challenge... is that the financing terms change on that current account. Increased cost to the economy - [a] consequence of that is a sharp slowing of the economy."
Mr Carney also refused to comment in detail on Monday's Treasury report which warned that the UK economy could be 6% smaller by 2010 if it left the EU, but said the report's "broad approach, to me, makes sense".
He said a vote to Leave "might result in an extended period of uncertainty about the economic outlook" which would be likely to affect demand in the short term and could affect the supply side economy.
Mr Carney's appearance in front of the committee comes just days after the Bank of England warned the EU referendum could hurt growth in the first half of this year.
The Bank warned uncertainty over the EU referendum could cause "some softening" in growth in the first half of 2016.
It also said sterling had also been affected by the uncertainty ahead of the vote.

Peacock joined Rovers at the start of the season, but was unable to help them avoid relegation to the Championship.
The 38-year-old came out of retirement in September, playing his fourth game of the season in Saturday's defeat.
"I always want to be accountable for my actions in life and offered my resignation after the game," he said.
"This was turned down which means I can continue my journey with this great club.
"While relegation hurts, it allows the club to stop just trying to change the branches and begin a full root-and-branch overhaul of the rugby department, building rock solid foundations that will enable this club to rise again."
Hull KR players had criticised the Million Pound Game format in the build-up, with their Super League contracts automatically becoming void as a result of their defeat.
"To be in a dressing room with grown men, wives and children crying is not what sport is about," Peacock added.
"To be part of a club with such loyal, passionate support is very humbling and the reaction after such a defeat will stay with me for life."

Up to 170,000 football fans are expected to travel to the capital to watch the showdown between Juventus and Real Madrid on 3 June.
It will be the first Champions League final to be played under a closed roof.
The Football Association of Wales (FAW) said safety was a "primary objective".
The roof closure had been suggested because of fears of a drone attack on what is described as the biggest club football game in the world.
After discussions with stakeholders, the FAW, said it had made the decision to close the roof after taking into consideration "recommendations made by the authorities".
The roof will also be closed for the two official training sessions to be held at the stadium on Friday 2 June.
Juventus and Real Madrid have been informed of the decision.
In a statement, the FAW said: "The 2017 UEFA Champions League final will be the first final to have been played under a closed roof and will further amplify the stadium's atmosphere when Juventus FC take on Real Madrid CF on Saturday 3 June."
It is the Bank's duty to talk about EU referendum risks, says Bank of England governor Mark Carney, dismissing accusations the Bank is too political.
[NEXT_CONCEPT]
Hull KR have rejected head of rugby Jamie Peacock's offer to resign following the club's defeat by Salford in the Million Pound Game.
[NEXT_CONCEPT]
The roof of the National Stadium of Wales will be closed for the 2017 Champions League final in Cardiff for safety reasons.