The organisation has delayed its reopening of 5k running events until 26 June over land permissions.
Weekly Parkrun events should be allowed to resume in England, cabinet ministers Robert Jenrick and Oliver Dowden say.
Writing to councils, the ministers said exercise was “vital” for physical and mental health.
The 5km local runs have yet to restart despite organised outdoor sport being allowed without a cap on numbers since 29 March under eased Covid rules.
On Friday, Parkrun said it had been forced to delay its planned reopening in England due to land permissions.
The organisation had hoped to restart events on 5 June after it was suspended due to the coronavirus pandemic, but fewer than half of its venues approved the runs.
It said 250 locations in England had given them permission to run on the planned date, but that this fell “far short” of the number needed to prevent overcrowding at the areas given the go ahead.
In a letter to all councils in England, the communities secretary, Mr Jenrick, and the culture secretary, Mr Dowden, said sport and physical activity were particularly important “as we recover from the pandemic”.
The ministers acknowledged the pressures that local authorities were under to consider requests for organised outdoor sports safely, but they stressed these events were exempt from legal gathering limits and could take place with any number of participants as long as they were in line with Covid guidance.
Around 150 landowners, including a number of local authorities, have either refused permission for Parkrun to return, or not yet replied to correspondence from the organisers, according to the letter.
It added: “Parkrun needs approximately 80% of Parkruns to be allowed to go ahead to prevent people travelling across the country from areas without a Parkrun operating, to ones which are.”
The letter said the government had been clear that Parkrun events were legally able to take place, with research showing mass-participation events such as marathons and fun runs can take place safely.
“In the interest of public health they should now restart,” it said.
“We therefore strongly urge local authorities to ensure that they are applying their powers in a consistent and proportionate manner and progressing Parkrun’s applications at pace in order to allow these events to return as soon as possible,” Mr Jenrick and Mr Dowden said.
Parkrun says it is hoping runs can resume on 26 June in Northern Ireland and on 3 July in Scotland. It is waiting to confirm a date for returning in Wales.