The Council of Europe has warned that asylum seekers in Ireland are being kept in facilities which have "negative consequences on their mental health, family ties and integration prospects".

Commissioner for Human Rights Nils Muiznieks said "asylum-seekers, in particular children, are spending a long time in facilities designed for short-term accommodation".

He said it will be an important step when Ireland finally adopts what it terms "long-awaited comprehensive asylum legislation" early next year, adding the current situation needed to be resolved.

The Commissioner was making his comments in a series of three letters to relevant Government ministers.

Minister for Justice Alan Shatter said he "very much looks forward" to publishing legislation on the issue of asylum seekers in the New Year.

Speaking in Brussels, he said the relevant legislation was currently "dysfunctional" and had been introduced in a "piece meal way".

He said that a "huge amount of work" had been completed by his department in preparing legislation, which would be "a radical reform" on what currently exists.

The Commissioner also welcomed the decision of the government to stop detaining children under the age of 16 in what it called "the outdated prison facilities of St Patrick's Institution".

The Council of Europe recommends transferring the remaining young offenders to facilities "where their educational needs can best be met".

Mr Muiznieks expressed concern that there is no "clear timeline" for the introduction of promised legislation on legal recognition of transgender persons.

The Commissioner said: "Five years have elapsed since a High Court's judgment found Ireland in breach of the European Convention on Human Rights in this field. The implementation process should be accelerated."

He called for a vigorous approach from the Government in upgrading domestic legislation regarding the rights of persons with disabilities.

While welcoming recent efforts, he said there was a need to review closely proposed budget cuts for their potential negative impact on the rights of persons with disabilities.

The Commissioner said that Ireland needs to ensure that its reform of the system for human rights protection is both strong and more compliant with international standards.

He said the Government needed to ensure that the ongoing merger of the Irish Human Rights Commission and the Equality Authority does not weaken the effectiveness and independence of national bodies to monitor human rights.

He said: "The independence of the new Commission should be clearly reflected in the way its members are appointed, the manner in which its staff is selected and recruited and in the arrangements for the allocation of its budget.

"It will also be important to ensure that the Equality Tribunal dealing with individual complaints under equality legislation be able to continue to fulfil its quasi-judicial function in an independent manner."

The Council of Europe has 47 member states, including Ireland, and the Commissioner's brief is to promote awareness of, and respect for, human rights.