Non-elite football clubs have been cleared to compete in the FA Cup this weekend despite new lockdown restrictions, but the Prime Minister has resisted calls to keep golf courses and tennis courts open.

Boris Johnson set out the terms for a second national lockdown over the weekend amid fears that a second wave of coronavirus cases would otherwise overwhelm the NHS this winter.

Grassroots sport will be forced to stop during the initial month-long period which starts on Thursday, which placed a question mark on whether FA Cup first-round ties involving 10 non-elite clubs could go ahead.

However, the Football Association said on Monday that the matches would go ahead under elite protocols.

“We can confirm that all Emirates FA Cup first-round ties will go ahead this weekend as planned,” a statement from the governing body read.

“The UK Government has confirmed that the 10 non-elite clubs that remain in the competition will be able to play their matches under elite protocols.

“Matches will take place between November 6 and 9 2020. All ties will be played behind closed doors, in line with COVID-19 guidelines.”

The FA confirmed the draws for the next rounds of the FA Trophy and FA Vase have also taken place, but no dates have been fixed.

“We remain in dialogue with the UK Government in relation to men’s ‘non-elite’ football in England and will release the fixture dates for both the Trophy and the Vase in due course,” a further FA update read.

The Government will order indoor and outdoor leisure and sports facilities including gyms, swimming pools, golf courses and driving ranges, climbing walls and climbing centres and archery and shooting ranges to close from Thursday.

The Prime Minister was asked whether golf courses might be exempted from the rules, given the socially distanced nature of the sport, by Conservative MP for Bracknell, James Sunderland.

Johnson responded: “I must apologise to my honourable friend for not being able to offer the house a huge list of exemptions to the rules we’ve set out.

“Because once you unpick at one thing alas the effectiveness of the whole package is compromised. That’s why I want everyone to work together for the next four weeks to get the R rate under control so that we can open things up again in time for December.”

A Government spokesperson said: “We recognise how important exercise is for people’s physical and mental health, which is why it has always been an essential activity under England’s coronavirus restrictions.

“From 5 November, indoor and outdoor grassroots sport facilities must close in line with the latest public health guidance. But outdoor exercise will be permitted alone, with your household, or one person of another household, so that people are able to stay active safely.”

Lawn Tennis Association chief executive Scott Lloyd labelled the clarification “hugely disappointing for all those who love tennis up and down the country” and vowed to “continue to put our case to (the Government)” ahead of the formal legislation which is due to be voted on in Parliament on Wednesday.

The chair of the Digital, Culture, Media and Sport (DCMS) committee, Julian Knight, had been among those calling for golf courses and tennis courts to be allowed to stay open.

Jane Nickerson, the chief executive of Swim England, said it was a “horrendous” situation and fears further facilities may never reopen.

“We’ve proved beyond a shadow of a doubt that indoor leisure and swimming pools have a very low transmission of this virus and are safe places for people to go and exercise,” she told the PA news agency.

“To just slam the door shut again now, my concern is that many pools won’t reopen and certainly I believe a lot won’t reopen now before Christmas. We’ve lost 200 swimming pools already following the first lockdown, I think an awful lot more can follow suit.

“We know that swimming is immensely valuable to the health of the nation. Our Value of Swimming report we launched last year showed that we save the NHS and social care system £357million a year on just six different conditions. And people who can’t exercise on land and can exercise in water, we’re just slamming the door on them.”

England Boxing chief executive Gethin Jenkins has warned of the “dire” consequences for clubs facing the prospect of another lockdown.

While professional boxing and the GB Boxing programme are set to continue under current regulations, the amateur side of the sport is set to be shut down.

Jenkins told the PA news agency: “If proper funding can’t be obtained, then the implications for our clubs is dire.

“A majority of our clubs operate in some of the most marginalised areas of the country and have been hardest hit.”

Former DCMS committee chair Damian Collins is among a group of MPs who have called on the Government to allow under-18s to continue participating in outdoor grassroots sport, including team sports such as football, when the new measures take effect.

In a letter to Culture Secretary Oliver Dowden, the MPs wrote: “Young people will currently be allowed to continue with sport at school, and we believe that the risks to the spread of coronavirus from outdoor grassroots youth sport would be minimal.

“There would however be clear and lasting benefits for these young people if the Government could support this.”

A petition has been set up calling for grassroots football to be allowed to continue during the new lockdown period.