A couple left in “agony” to fight against the enforced adoption of their three-year-old son could be forgiven for thinking they are trapped in a system which is “neither compassionate nor even humane,” the most senior family court judge in England and Wales has said.

The child was removed from his parents nine months ago by Swindon borough council and placed in temporary foster care. But for the past 10 months, the couple have been struggling to get the legal aid without which, said Sir James Munby, president of the family division of the high court, they would be left in the “unthinkable” situation of facing the local authority’s application without proper representation.

Munby called the delay unconscionable and said the parents had been left in a shocking predicament.

He said: “Whatever the administrative excuses, the human reality is that a little boy has been separated from his parents pending a final decision for far too long – and for a period which is manifestly excessive.”

The legal aid application process is, said Munby, a “barrier to access to public funding” for people who lacked mental capacity.

“The complexity of the process involved in obtaining legal aid for [the boy’s] parents is, quite manifestly, beyond their capabilities,” he said. “This state of affairs is … both unprincipled and unconscionable.”

He added: “A parent facing the permanent removal of their child must be entitled to put their case to the court, however seemingly forlorn, and that must surely be as much the right of a parent with learning disabilities … or a parent who lacks capacity … as of any other parent.”

Munby said the couple had now been granted public funding and the legal aid issues had seemingly been resolved, and a final hearing is due to take place next month. However, he warned, there is “as yet no assurance” that legal aid would be in place for the final hearing of issues relating to the three-year-old’s future.

The couple had initially been disqualified from receiving legal aid because the father earns £73.94 a month too much to qualify. But Munby said he was disturbed by the fact that the couple had not qualified for legal aid and yet did not have enough money to pay lawyers.

“Even those of us who spend our lives in the family courts can have but a dim awareness of the agony these parents must be going through as they wait, and wait, and wait, and wait, to learn whether or not their child is to be returned to them,” he said.

“The parents can be forgiven for thinking that they are trapped in a system which is neither compassionate nor even humane. Is this really the best we can do?”

Munby had suggested last October that the justice secretary and lord chancellor, Chris Grayling, should consider the couple’s case. Justice minister Shailesh Vara later wrote to the judge outlining Grayling’s position. “I acknowledge that in this case, the parents and their representatives have faced considerable uncertainty for some time over the legal aid position. However, it is a necessary feature of means and merits testing that legal aid cannot be made available until information has been provided which shows that the statutory tests have been met.”