By law, employers must protect workers from smoke
The code of practice, which must be approved by ministers, would be compulsory, and would replace the current voluntary approach.
Employers who breach the code could find themselves in court.
The HSC decision follows a public consultation on the issue.
Many companies have already introduced smoking bans for fear of being sued by employees over the effect of passive smoking on their health.
But the HSE is concerned that one in five businesses still has not done enough to control smoke in the workplace.
In pubs and clubs the new rules will not mean a complete ban on smoking.
But to protect staff, customers may be stopped from smoking at the bar, and employers may be forced to install expensive ventilation systems behind the counter to avoid prosecution.
Pubs and clubs will be given two years to comply with the new rules.
However, the industry argues that is not enough, and that small businesses, in particular, could be under threat.
Mark Hastings, of the Brewers and Licensed Retailers Association, said: "The problem with regulation like this is that it is very heavy handed and does impose an almost instant cost on the business.
"We would prefer to stick with the voluntary code which is working. We are actually ahead of target for what we are trying to achieve by 2002."
'Very important measure'
Amanda Sandford, from the anti-smoking charity Action on Smoking and Health (Ash) said: "This is a very important measure.
"It will go a long way towards protecting the health of approximately three million people who are exposed to passive smoking in the workplace."
Ms Sandford said the evidence that passive smoking damages health was overwhelming.
Most employers already had smoking policies in place, she said.
However, Simon Clark, director of the smokers' rights group Forest, said the move was motivated by political correctness.
"A code of practice will create a less tolerant and more divisive society.
"Employers have to be given the freedom to come up with a policy on smoking that best suits their business."
He said employers could easily accommodate smokers by providing smoking rooms, and well ventilated areas.