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The association also claims that the changes are unlikely to raise the desired £3.1bn in additional taxes.
The NAPF has written to a number of MPs urging them to consider the wider impact of the pension changes, as it claims that while the proposals are directly aimed at the UK's 230,000 highest earners, their impact is likely to be felt by more modest earners in the medium term.
The organisation has already given evidence to the House of Lords Economic Affairs Sub-Committee to outline its concerns.
According to the NAPF, the proposals break the long-established EET2 principle on which UK pensions have been based, by withdrawing tax relief on employee contributions and imposing a tax charge on an individual's employer contributions.
The NAPF is therefore concerned that by having broken this principle, there is a risk that future governments will make the same changes for those on lower incomes.
The proposals also break the tax simplification framework - introduced by Labour in 2006 - which was intended to be a lasting settlement.
The NAPF said such constant changes to legislation could do nothing but undermine scheme sponsor confidence in the stability of, and government's commitment to, pensions.
In addition, it has argued that the proposals ignore the fact that higher earners will also tend to pay tax at higher rates when they retire.
According to government figures, 210,000 pensioners paid higher rate tax, a similar number to the 230,000 who will be affected by these changes. So the tax treatment of pensions is better seen as tax deferral.
The people directly affected by these changes are likely to be those making decisions about company remuneration policy. Should these people become disengaged from company pensions there is a risk that lower earners could be negatively affected.
The NAPF has also expressed doubts that the Budget measures will raise the £3.1bn in additional tax revenue HM Treasury predict as individuals seek more tax efficient ways to save and companies look to new ways to reward higher paid staff.
Joanne Segars, chief executive at NAPF, said: "The Budget changes send out the wrong messages on pension saving. The government must think again about the wider impact of the new measures as the changes are likely to affect more than just top-rate tax payers.
"The government's proposals break a long established principle tax policy in this country and the constant instability in legislation does nothing to help rebuild badly needed confidence in pensions."
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