The incident happened in the city, as residents took to the street to demand the resignation of President Omar al-Bashir.
The 74-year old has been in power since a military coup almost 30 years ago.
There was no report of casualties during the incident.
“It’s unacceptable for security forces to storm hospitals” said Health minister, Mamon Hamida was quoted by local reports on Saturday.
He said measures had been taken following the incident including police protection for doctors, patients and staff at the hospital.
A video posted on social media shows patients and families taking refuge in emergency rooms and complaining about the teargas which had enveloped the Omdurman teaching hospital.
Soldiers beat doctors inside the hospital and made some arrests, according to a statement by the Sudanese doctors association.
Last Wednesday, three protesters were confirmed dead and 12 others injured as thousands took to streets, one of the biggest protests in Omdurman.
The attack on the hospital caused international outrage with Amnesty International describing it as an outrageous violation.
Sudan’s nationwide demonstrations started on 19 December over the rising price of bread before it quickly turned into a political movement demanding regime change.
Tens of thousands took to the streets in over 20 cities, leaving 22 protesters killed according to official figures.
The opposition however put the death toll at 47.
At least 3, 000 have been arrested.
The marches called by Sudan’s Union of Professionals in collaboration with opposition parties have vowed to exert increasing pressure on President Bashir to resign.
The Sudanese economy has been in dire straits since South Sudan seceded from the rest of the country, taking with it nearly 75 percent of oil fields.
Inflation recently jumped to 66.82 percent despite the lifting of US-led sanctions which had been in place for twenty years.