In part this difference in focus can be explained by the fact that revenue administrations are less focused on policy. Revenue administrations are by and large process-oriented institutions, especially if tax policy studies and proposals are undertaken by a separate institution. PFM processes are much more policy development and implementation oriented. The preparation of the budget is an annual process requiring a lot of analysis, negotiation, creative thinking......and elbow grease. The belief is often that despite changing the preparation process, the process should still be accommodated by the same organizational structure and staff complement. This fallacy occurs especially with the introduction of MTEFs and program budgeting; in treasury modernization the institutional angle is often taken better into account. Changing the budget classification and appropriation structure to a programmatic one, for example, is sometimes only seen as a presentational issue. Some more work for the budget office, but nothing major.
However, compiling the budget on a programmatic basis requires considerably different and more extensive staff capacities. Budget office staff need to understand line ministry policy objectives and implementation strategies much more fundamentally then under input budgeting. They need to engage in a meaningful discussion with their line ministry counterparts in a way that input budgeting never required. Ministries of Finance often discover that the type of staff in the budget office has to change considerably with respect to educational background, and also that staffing levels need to be expanded. With input putting, where budget determination is largely an incremental exercise - with some consideration of changing input costs - one budget officer can often cover several ministries. In program budgeting, ideally several staff members are attached to each major ministry.
For ministries of finance, recognition of these needs is often difficult. Ministries of finance around the world pride themselves on having the best and the brightest staff in the civil service. This is often true. They sometimes also have some of the most stubborn! The pride in their own capacities leads to the mistaken believe that they can tackle any challenge thrown at them. On top of that, it is of course often very difficult for ministries of finance to argue for expansion of their own staff, when staffing levels in line ministries are being cut. However, program budgeting requires a strengthening of the center of government, to make effective use of new information and analysis, especially once a performance framework is added to the program classification.
The end-result of not adapting staffing composition and levels is that program budgeting reforms in finance ministries often do not have the desired effects. This in turn has the consequence that old processes are kept alive, or on standby, as a sort of security blanket. Good old input budgeting is still used to save the day!
Ideally, introducing program budgeting should also be accompanied by rethinking of the organizational structure of the MOF. It often makes sense to split the Budget Office in a expenditure directorate and a budget directorate more focused on budget aggregates and overall process management. Span-of-control and work specialization are the main reasons for such proposals. Again such changes are often difficult due to the strong corporate culture in ministries of finance, and the hesitancy to submit such proposals to civil service commissions (who can be extra critical of ministry of finance requests).
In comparing PFM reforms to Revenue Administration reforms, one of the striking features is that reforms of the budget process are often attempted without much consideration of the institutional changes that are required. MTEF and program budgeting reforms are often implemented with only limited changes to capacities and institutional structure of ministries of finance (or line ministries). The changes to the budget process that these reforms imply are quite fundamental however, and do require changes in staffing level, professional capacities and organizational structure. 
