Boris Johnson is being asked for urgent reassurance over jobs at the Scottish-based Department for International Development (DfID).
The prime minister has announced a merger with the Foreign Office (FCO) to create the new Foreign Commonwealth Development Office.
He said the "long overdue reform" would ensure "maximum value" for taxpayers.
But the move has prompted fears for 948 staff at the DfID headquarters in East Kilbride.
As part of his "Global Britain" address to the House of Commons on Tuesday, Mr Johnson told MPs combining DfID and the FCO would "unite our aid with our diplomacy".
Downing Street sources indicated there would be no compulsory redundancies.
But local MP Dr Lisa Cameron said she wanted guarantees staff would be protected.
The DfID has been based at Abercrombie House in the new town since the 1980s and is believed to produce £30m for the local economy.
In 2010, the DfID's Overseas Territories Department (OTD) was relocated from London to boost the workforce in East Kilbride.
The department has played a key role in tackling Ebola, gender inequality, the crisis in Syria and the provision of lifesaving aid in emergencies.
Dr Cameron told the BBC: "Boris Johnson must commit to protecting jobs in DfID's East Kilbride base - it is one of Whitehall's biggest footprints in Scotland and its work highly thought-of worldwide.
"The PM must deliver a public guarantee that these jobs are secure and that they will stay in East Kilbride. I will be writing to him requesting urgent reassurance for local DfID staff."
The SNP's Westminster leader Ian Blackford accused the prime minister of "playing politics" by announcing the changes during the Covid-19 crisis.
Mr Blackford said: "The prime minister and this UK government are using the cover of a terrible pandemic to rip apart the UK's structures for international development and humanitarian aid at a time when we should be standing with the world's poorest, acting as a beacon of hope.
"The prime minister is playing politics."
He called for a "cast-iron guarantee" that the jobs were secure and would stay in East Kilbride.
Mr Johnson replied: "Of course we are going to keep the jobs in East Kilbride. Of course we are going to support the work of those fantastic people in East Kilbride."
The prime minister said work would begin immediately on the merger and the department would be formally established in early September, with Foreign Secretary Dominic Raab in charge of the new-look operation.
However, the Public and Commercial Services union (PCS) said members at the East Kilbride site were very worried about their job security.
They were told verbally that the building would remain in the new department, but the union is seeking a written assurance on this point.
PCS general secretary, Mark Serwotka said: "This has come to a shock to staff who, disappointingly, only learnt of the news through leaked reports made before the announcement in Parliament.
"Such a major change will be costly and take months of planning. Yet the PM expects it to be up and running within three months in the midst of a national crisis.
"There has been absolutely no consultation with the trade unions and we are concerned that this merger is driven by cutbacks and not about making improvements to international aid and diplomacy."