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.
Labour's former culture secretary Ben Bradshaw, who is an ex-BBC journalist, said the corporation should publish any evidence it has that it obtained permission from students.
Mr Bradshaw, who sits on the Commons culture committee, added that programme makers should have gone "even further" than usual to get permission and said he was "amazed" they did not secure written consent.
He told BBC Radio 4's World At One programme: "Central to the BBC's editorial guidelines is the principle of informed consent."
The BBC has been saying that they fully explained the risks to the students and that any risks that there could have been were justified.
Some of the students that went on the trip have via the student paper, Facebook and through friends been saying that they did not think they were fully informed of the risks.
One student said: "I was never told there would be a documentary that would implicate me before we landed in North Korea."
They believed that BBC Panorama reporter John Sweeney was a history professor at another university until halfway through the trip.
This has gone right to the top of the BBC, with the new director-general Tony Hall making the decision that the Panorama programme should go ahead despite what the London School of Economics want.
He is in front of MPs next week and we know that they want to question Mr Hall about this incident and some are saying that there are some problems for the BBC in what has happened over this.
Ceri Thomas denied that the briefing of the students had been "shambolic" and rejected claims that students had been forced to run unacceptable risks during undercover filming of the investigation.
He said: "We think the risks as we explained them to the students were justified.
"But I need to be absolutely clear that if we had any suggestion that lives were at risk or anything approaching that - either the BBC team's lives or the lives of the students - then we wouldn't have gone anywhere near this."
Asked whether the then-acting director general Tim Davie had signed off on the plans, Mr Thomas replied: "I can't be sure that Tim Davie did. I know that Tony Hall (the current director general) has been involved in recent days."
The BBC has been accused of putting a group of students in danger over an undercover documentary about North Korea.
A Panorama reporter used a study trip from the London School of Economics as cover for secret filming inside the country.
The BBC claimed the students involved were fully briefed, but the university says it was kept in the dark about the deception.
ITV News reporter Martha Fairlie reports:
The chief executive of Universities UK, Nicola Dandridge, said they are "concerned about the methods used" in the making of the BBC Panorama programme, after an academic trip with LSE students was used to gain entry to North Korea.
Ms Dandridge said universities must be able to work with integrity and operate in sensitive areas of the world.
"The UK's academics have a global reputation, and it is vitally important that they can be trusted and seen to be working in an open and transparent manner", she said.
"The way that this BBC investigation was conducted might not only have put students' safety at risk, but may also have damaged our universities' reputations overseas", Ms Dandridge continued.
"We regret the BBC's approach in this matter. Universities UK will be seeking to discuss this with the BBC to ensure they fully understand the concerns of the university sector".
The head of the LSE student union has attacked the BBC accusing it of organising a student trip to North Korea "potentially as a ruse for them to get into North Korea".
Alex Peters-Day told BBC News: "We don't know what could have happened to those students [if it had been discovered that were accompanying BBC journalists] and crucially neither does the BBC".
She called on the BBC to pull the programme, which is due to air on Monday, and also demanded a full apology.
Panorama reporter John Sweeney has defended his actions after using an academic trip with LSE students to gain entry to North Korea.
Sweeney told the BBC:
When asked why the students had only been told of a single reporter going on the trip, when in fact there were three, Sweeney, his wife and a cameraman he said: "If I was arrested, then the less the students knew the better, the majority of the students are supportive of the documentary."