MPs have passed amendments to the government’s latest counter-terrorism bill to try to protect British aid workers and journalists from facing criminal charges in conflict zones.

The controversial draft bill, aimed at tackling Isis fighters travelling abroad, allows the home secretary to declare somewhere a “designated area” and make it an offence for UK nationals and residents to be there. The bill orginally allowed individuals – including humanitarian workers, journalists and academics – to be investigated by the police and ultimately face 10 years in prison.

But following calls from 22 leading humanitarian groups – including Christian Aid, and Oxfam – to exclude aid workers and others, Lord Rosser proposed exemptions including humanitarian workers and journalists. The bill, which returned for a Commons vote on Tuesday, has also drawn criticism from campaigners on freedom of expression.

Jan Egeland, head of the Norwegian Refugee Council, welcomed the amendments: “This bill reached public debate in the shape and form that would criminalise my British colleagues who are in areas with greater suffering and where they are trying to help victims of terror. It’s symbolic of how it’s becoming more difficult to do traditional civilised humanitarian work for those in greatest need, irrespective of where they are.”

Dr Rowan Popplewell, advocacy adviser at Bond, which represents more than 400 international development groups, welcomed its passing, but urged the government to exempt other working groups, including peacebuilders.

“On balance we support the amendment. It is better than what was there before. However, there are categories that are missing, including development researchers, academics and peacebuilders. We would like the government to seriously think about adding more exemptions, and we will be talking to them about that.”

Stephen Twigg, chair of the international development committee, said it was “important that we strengthen legislation to tackle terrorism” but it would be sad if an “unintended consequence” would be to limit citizens’ rights to work in fragile states.

Exemptions also include UN workers, those carrying out work for a country other than the UK or those attending the funeral of a relative or one who is terminally ill. Ben Wallace, the security minister, said he would keep the list of exemptions under review and that he was “confident that genuine peacebuilders will have a reasonable excuse”.

Joy Hyvarinen at Index on Censorship said the bill remained “fatally flawed”.

“Even after the small improvements that passed today, I remain very concerned that large parts of this legislation are going to reshape the law on freedom of expression and freedom of the press in the UK, and I expect there to be court challenges.

“There is a whole pack of measures relating to the borders and a lot of people are very concerned about the lack of protection for journalists in that package.”

Hyvarinen and others have flagged concerns over plans to criminalise the viewing or publication of online content that is likely to be useful for terrorism, which they say would impact on academic researchers and investigative journalists.