David Cameron and Nick Clegg should agree and publish a set of "rules of the game" for developing policies in the last year of the coalition Government, a Whitehall think tank has said.
The Institute for Government (IfG) warned there was a risk of "unfairness" to the Liberal Democrats in drawing up policies with the aid of civil servants, because the Conservatives run more ministries.
The report, based partly on anonymous interviews with senior civil servants, found in some departments ministers from one party would explicitly try to exclude the other from policy discussions.
The IfG called for the Prime Minister and Deputy Prime Minister to agree how the process of policy development should work in the final year of the coalition, when the parties will be developing proposals which could potentially find themselves in rival election manifestos.
The report notes that the civil service should maintain a clear divide between government and party business, but in a single-party administration "officials are often asked to carry out analysis or provide advice on policy ideas that the party of government is considering for its manifesto".
In a coalition this "grey area" becomes more complicated, with officials potentially being pulled in two different directions by competing ministers.
The report found that the way Whitehall coped with the coalition varied from department to department, often depending on the personality of the secretary of state.
It highlighted the controversy over the immigration advertising vans in the Home Office as a situation where "an actual policy pilot was rolled out without consultation with the other party".
In some ministries there was a culture of openness but in others policy development was sometimes carried out solely by one party "occasionally with explicit requests not to include the other side in discussions".
The report said: "There is a lack of clarity in such circumstances about whether policy is being developed for the Government, or for one party.
"This can also strain working relations within a department. In one case a secretary of state instructed officials to keep junior ministers out of the loop because of concerns they would pass on sensitive information to the party leader."
The IfG said Mr Cameron and Mr Clegg should agree and publish clear rules for the final year of the Government.
These should include "rights of access" for each party to civil service support for policy development, how the two sides will reach "agreement to disagree" and the "terms of engagement" between the Tories and Lib Dems to avoid surprise attacks within the Government.
The report recommended following the example of Scotland in 2007, where Sir John Elvidge, the then permanent secretary, presided over a system known as "separate space" where each coalition party could request information from officials but under clear rules and with the guarantee of confidentiality.
The IfG said this system should operate in parallel with the pre-election contact offered to the Opposition, which Mr Cameron has said will not commence until October this year.
"To ensure fair treatment, the coalition parties should also not be able to access private support to be able to develop post-2015 policy until that point," the report said.
In the foreword to the report, IfG director Peter Riddell said: " There is an obvious risk at present of unfairness to the smaller party, especially when most departments are headed by secretaries of state of the larger party.
"But a broader danger for government is that, without clearer guidelines, caution will prevail and insufficient work will be undertaken on post-2015 policy options in areas of disagreement within the coalition."
He added: " Civil servants already report that they are being put in a very difficult position as - in the absence of guidance from the centre - they try to work out how to give advice to ministers from different parties without being, wholly falsely, seen as favouring one party or another."
The IfG was critical of Mr Cameron's decision not to grant Labour access to the civil service until October, saying that for future elections the pre-election contact with the Opposition should begin 10 months to a year before polling day.
A Cabinet Office spokesman said: "It is important to be clear that the constitutional position of the civil service is to serve the government of the day. The coalition works well with the civil service, which is supporting ministers from both parties.
"The Civil Service Code makes clear the duties and responsibilities of civil servants. There is no confusion about this. As has always been the case, departments are often asked to do some work for individual ministers despite working for the Government as whole.
"The introduction of a fixed-term parliament has removed the previous uncertainty over the length of pre-election contacts - they will now start on 1 October 2014, which guarantees seven months of contact. Further guidance will be issued in due course."