The new Prime Minister has been making sweeping changes to the ministerial line-up since he moved into Number 10 on Wednesday.
David Westwood, Director of Policy and Programmes at World Vision UK said in a statement: "We know that aid is spent most effectively and transparently through DFID, and we urge Sharma to fight for it to remain an independent department.
"A messy and costly merger with the foreign office would lead to inefficient spending, unclear priorities, and a waste of taxpayers' money.
"When aid is spent well it helps break the cycle of poverty. But it's also a key part of building the UK's influence on a global stage, while helping ensure peace and stability.
"A government that claims to promote a 'global Britain' should take this seriously."
The Christian charity recently presented the Department for International Development (DFID) with a petition, urging it to increase spending to stop children being abused in disaster zones.
More than 34,000 people around the UK signed.
"Sharma has a real opportunity to ensure that UK Aid continues to prioritise the world's most vulnerable children and their communities – especially in fragile and emergency contexts," Westwood added.
"It is crucial that he maintains the 0.7 per cent aid budget, and puts a focus on the causes of humanitarian emergencies such as conflict and the climate crisis.
"We look forward to working with him to help empower children, and save lives."
Sharma has said he is "delighted" with his new appointment.
He added: "I am committed to transforming the lives of the world's poorest and most vulnerable people, giving them access to quality education and jobs, while promoting Britain's economic, security and foreign interests."
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