When Jo Swinson, the Deputy Leader of the Liberal Democrats, alleged that Brandon Lewis had broken a pair during the crunch vote on the trade bill, both he and Julian Smith, the Chief Whip, were quick to claim that it was an honest mistake.

There was already an obvious hole in this account – that Lewis only voted during the most important and closely-fought divisions, and not on the third reading – when this morning’s Times alleged that Smith had “urged three Tory MPs to abandon “pairing” arrangements”. The other two reportedly sought further advice and then ignored the instruction.

Suffice to say, it looks bad, with the Sun reporting that Theresa May “condemns her own party whips”. She has also issued a “full apology” and said that the Government will consider introducing a proxy vote system for female MPs with young children. Smith is being called upon to give a statement to the House.

Thus far no denial of these new claims has been forthcoming on Smith’s Twitter feed, nor from anybody else whom we have approached. Unless one is forthcoming, and with it a convincing alternative account of yesterday’s events, then pressure will mount on the Chief Whip to consider his position.

Beneath the adversarial public performances, Westminster runs on trust. The pairing system might seem arcane but it is a crucial part of how our legislature functions, allowing MPs with pressing commitments elsewhere – be they government business, an illness, or a young child – to miss votes without letting down either their electorate or their party.

Important as yesterday’s vote on New Clause 18 (Stephen Hammond’s custom union amendment) was, the pairing system is sacrosanct. If it collapses the Government faces the prospect of having to keep every last MP – including the Democratic Unionists, over which it has no direct authority at all – as close to London as possible at all times.

Even without a 1970s-style collapse on that scale, an angry Opposition still has much greater scope for immiserating the Government with procedural chicanery (dragging out business, pushing for late sittings, stalling in committees, and so on) than vice versa. With the parliamentary arithmetic already razor thin and one of the Government’s Northern Irish allies facing suspension and possibly a by-election, the last thing it needed was to make an already difficult Commons environment actively hostile.

May currently seems minded to allow Smith to continue in post. There are arguments for this: for one, she can scarcely afford another angry backbencher; for another he is the longest-serving and most experienced member of the whips’ office (itself a minor scandal). But the Chief Whip must command the trust and respect of both his own MPs and his opposite numbers to do his job. At this point, that looks a tall order for Smith.

Update: As of 5pm, the Times is reporting that Smith “told a rival chief whip that he deliberately intended to break the pairing system”. He reportedly apologised for breaking Swinson’s pair as she was on ‘pregnancy leave’, saying he would have chosen another had he realised.