Comic Relief chief executive Kevin Cahill, speaking on BBC Radio 4's World At One, accepted that Comic Relief had a "small percentage" of cash in areas such as tobacco and arms firms through managed funds.
"There's no more than 5 percent of our funds in those particular areas," he said.
After being told ethical funds had outperformed FTSE 100 companies index over recent periods, he said: "Our trustees were acting in good faith in what they were doing.
"It's very good to hear that, in fact, the potential exists within ethical funds to match the return because Comic Relief would clearly choose to be in those if the return was equal or better to where we currently are so it's a no brainer for us to be in those funds."
Comic Relief - which has been criticised for its dealings with the tobacco and arms industries - has avoided a policy of ethical screening for its investments because the charity says it does not want to limit the amount of money it raises.
BBC Panorama highlighted that Comic Relief had £630,000 in shares in BAE Systems, a leading weapons manufacturer, in 2009 despite having a mission statement which talks of a commitment to help "people affected by conflict".
The charity has also given money to help the fight against tuberculosis but had £3 million of its money wrapped up in tobacco companies in the same year, even though smoking is said to be a contributory factor in many TB cases.
And although it aims to reduce alcohol misuse and its spin-off effects, the charity had £300,000 invested in the drinks industry in 2009. Panorama said Comic Relief refused to reveal its current investments.
Comic Relief is to conduct a "full review" of its investment policy after the charity was criticised for its dealings with the tobacco and arms industries.
A BBC Panorama programme screened last night highlighted the money that the charity has tied up in some areas which appear to run counter to its aims because it does not exercise any sort of ethical screening on its investments.
But chief executive Kevin Cahill said that it will look again at where it puts its funds in order to do "the right thing".
BBC1's documentary claims Comic Relief could have generated more cash from shrewd investments in "ethical" funds.
The charity, which generates huge publicity for its activities with star-studded programmes screened by the BBC, has avoided a policy of ethical screening for its investments because it says it does not want to limit the amount of money it raises.
A politician's "spur of the moment" charity idea left her more than £14,000 down after promising £1 for every retweet she got on Twitter.Read the full story ›
Once again the extraordinary generosity of the British public has put Comic Relief in a position to be able to serve thousands upon thousands of people with very hard lives in Africa and the UK.
It's almost impossible to thank enough all those who took part in the event, all the members of the public who fund-raised and all those who gave so generously on the night.
This year's Comic Relief has raised a record £75.1 million so far, beating 2011's total of £74.3 million.Read the full story ›
Ricky Gervais returned to our screens as David Brent last night, all to raise money for Comic Relief.
The special shows what happened to Brent 10 years after The Office ended.
Taking to Twitter, Gervais wrote, "Thank you for all your amazing comments about Brent's Return. I had a blast".
Jessie J has thanked her fans for donating to Comic Relief after having her head shaved live on television to raise money for the charity.
She wrote on Twitter, "I am soooo thankful to everyone who has donated @rednoseday and supported me tonight! My heart is filled with with happiness! Lets make a change! X"
The singer said shaving her head "is the smallest thing I can do to give back to these people who need it so much".
Jessie J has raised more than £500,000 so far by having her trademark locks shaved off.
Fiona Mactaggart MP has pledged to donate £14,268 to Comic Relief, after saying she would donate £1 for every retweet she received before 9 pm of a tweet sent earlier this evening at 8:25 pm.
Ok stop now I owe comic relief£14,268. Phew! Cheque soon if you don't believe me check with comic relief
Fiona MacTaggart, MP for Slough, has pledged to donate £1 to Comic Relief for every retweet she receives for the tweet posted below before 9 pm.
At the time of writing, the tweet has received thousands of retweets.
I will give £1.00 to Comic relief for every retweet of this message before 9pm