The UK should withdraw from the Council of Europe if it chooses to ignore pan-Europe judgments giving prisoners the right to vote, the continent's most senior human rights official has warned.

Niels Muižnieks, the Council of Europe's human rights commissioner, said British MPs could not "cherry-pick" decisions issued by the European court of human rights.

His comments, published in evidence to the joint Commons and Lords parliamentary committee considering the draft voting eligibility (prisoners) bill, are likely to raise the political stakes in an already inflamed confrontation that has set British ministers at odds with the Strasbourg-based European court of human rights.

The court first ruled in 2005 that a blanket ban preventing all prisoners from voting in elections was incompatible with human rights.

Having failed to persuade the ECHR judges to reverse their decision, the government published a draft bill last year setting out three political options: a ban for prisoners sentenced to four years or more, a ban for prisoners sentenced to more than six months, and a restatement of the existing ban – in effect defying Strasbourg.

Muižnieks' letter, addressed to Nick Gibb MP, chair of the parliamentary committee looking at the draft prisoners voting bill, says: "If the UK, a founding member of the Council of Europe and one which has lost relatively few cases at the Court, decides to "cherry-pick" and selectively implement judgments, other states will invariably follow suit and the system will unravel very quickly.

"Thus, my message is clear: the Court's judgments have to be executed and the automatic and indiscriminate ban on voting rights for prisoners should be repealed. If the court system is to continue to provide protection, there is no alternative to this for member states, other than leaving the system itself.

"It seems likely that the UK's voice in the broader UN human rights system would also be negatively affected by a withdrawal from the Council of Europe. As a permanent member of the Security Council, the UK has additional responsibilities within the UN system.

"A withdrawal from the ECHR would cast doubt on the UK's commitment to UN values and acceptance of UN mechanisms such as the Universal Periodic Review and treaty monitoring bodies. The UK's voice with regard to human rights issues in other countries would clearly be less credible.

There are 47 members states in the Council of Europe, including Russia, Turkey, Ukraine and Albania. The only European nation that refuses to join is Belarus, whose human rights record has been widely criticised.

In November, the government published the voting eligibility (prisoners) draft bill for pre-legislative scrutiny by a joint committee of both houses.