Release International is calling upon William Hague to speak up for human and religious rights in talks with Egyptian and Syrian authorities.
The rights group welcomed assurances from new Egyptian President Mohammed Morsi that religious freedom will be safeguarded.
However, Release said that Christians in Egypt still fear an increase in persecution after the election of the Muslim Brotherhood candidate.
Extremist groups such as Al-Gama’a al-Islamiyya and Egyptian Islamic Jihad pose an additional threat with their goal to introduce strict Sharia law across Egypt.
The concerns have prompted an estimated 100,000 Christians to leave Egypt since the uprising.
Release said the departure of so many Christians had left those remaining feeling "increasingly vulnerable".
Release UK Director Colin King said: "Judging by the exodus of Christians from Egypt, many remain unconvinced. They are looking to President-elect Morsi to protect their security and guarantee their freedoms.
"Release is pleased the British Foreign Secretary has raised the issues of human rights with the Egyptians and we continue to impress on him the need to keep religious freedom at the top of the agenda in any talks."
In Syria, members of the Christian community have been caught up in the ongoing conflict between rebels and forces loyal to President Bashar al-Assad.
Under al-Assad, Christians enjoyed relative religious freedom. Now they fear that regime change could lead to an increase in persecution by Islamist militants, similar to the experience of Iraqi Christians after the fall of Saddam Hussein.
Christian groups working in the country have reported attacks on Christians, including kidnap and murder, since the start of the uprising.
According to the World Evangelical Alliance’s Religious Liberty Commission, extremist Islamist forces in the opposition movement have attacked Christians suspected of backing al-Assad.
The Syrian Orthodox Church has claimed that there is an "ongoing ethnic cleansing of Christians" by suspected members of an al-Qaeda-linked group in Homs. Reports indicate that 90 per cent of Christians in the city have fled to Jordan and that their homes have been seized by militants.
Release wants Mr Hague to take action to ensure that Christian minorities in Egypt and Syria are protected.
It has launched a letter-writing campaign to the Foreign Secretary expressing "deep concern about the future of human rights for minorities, especially Christians in North Africa and the Middle East in the wake of the Arab Spring revolutions".
"We want to urge Mr Hague to place the protection of minorities at the forefront of talks with emerging rulers in the Arab Spring nations," said King.
"We’re asking him to continue to do everything in his power to seek assurances regarding their human rights."
Release is also supporting safe houses in North Africa and the Middle East that are providing emergency accommodation to Christians that have been attacked or forced to leave their homes.
"Christians in North Africa and the Middle East need our prayers and financial support more than ever," said Mr King.
Concern for Christians in Syria and Egypt
Published 28 June 2012