The council’s local plan was submitted for examination in March by the local authority's previous Conservative administration.
Local elections in May saw control of the authority pass to a coalition of Lib Dems, Greens and independent councillors, many of whom were elected after campaigning against the local plan.
Last week, the council’s cabinet resolved to scrap the existing plans and begin work on fresh proposals.
The cabinet decision was due to be discussed at a full council meeting this evening (10 October), during which a vote to pull the local plan and begin again was scheduled to take place.
But Robert Jenrick has now written to the Lib Dem leader of the council, Sue Cooper, ordering the authority "not to take any step in connection with the adoption of the plan".
In his letter, dated 9 October, Jenrick warned the council that taking the plans back to the drawing-board would be "likely to create uncertainty and expose communities to speculative planning applications".
The minister also said that "progressing the plan is an essential step to delivering the Oxfordshire Housing and Growth Deal", through which £215 million of infrastructure funding would be provided by Whitehall to the county.
The letter makes no mention of the future of the council’s share of a separate pot of £218 million of funding from the government’s Housing Infrastructure Fund (HIF) for infrastructure intended to enable new housing across the South Oxfordshire and the Vale of White Horse districts.
He added: "I would like to work constructively with you to ensure that South Oxfordshire is able to deliver the high-quality homes and infrastructure to support jobs and growth in the local community."
The letter says the direction in relation to the plan will "remain in force until I withdraw it or give a direction" under section 21 of the Planning and Compulsory Purchase Act 2004.