The milestone came as the health ministry announced another 42,360 new cases over the past 48 hours, taking the overall figure to 2,024,904.
But seroprevalence studies, that test people using a blood serum sample, suggest the figure is far higher.
“The total number of confirmed cases… already exceeds two million today,” said Maria Jose Serra, deputy head of the health ministry's emergencies unit.
“Clearly, we are seeing a new increase of cases, they had decreased and now they are increasing again in what we could call the third wave,” she said.
Over the same 48-hour period, Spain also saw another 245 deaths, raising the overall toll to 51,675. And the incidence rate also shot up, rising from 296 cases per 100,000 people to 321, the figures showed.
Datos sobre #COVID19 en España, desde el primer caso inicial, actualizados a hoy jueves, 7 de enero:
▶️Confirmados por PCR: 2.024.904
— Salud Pública (@SaludPublicaEs) January 7, 2021
On October 21st, Spain became the first European country to record a million coronavirus infections, with Prime Minister Pedro Sanchez admitting just days later that the real number was three times higher.
And in mid-December, a new seroprevalence study suggested around 4.7 million people had been infected by the virus — or around 10 percent of Spain's population.
Although the numbers have shot up, prompting most of Spain's 17 regions to impose new curbs on public life, the government has remained adamant it won't impose a new lockdown.
Jose Serra also said Spain had identified “around 60 confirmed cases” of the highly-contagious coronavirus variant which is sweeping Britain, but said it was not a key driver in the recent surge.
'No plans for new lockdown'
With infection spreading rapidly across Europe, many countries have been forced into a second or even a third lockdown, but Spain has so far insisted the restrictions put in place under its state of emergency are sufficient.
“It's not in our sights, nor is it a measure we are contemplating,” said Illa earlier on Thursday.
Memories of the harsh months-long lockdown imposed last March remain fresh in Spain where no one was allowed out for walks or exercise for six weeks until the government began slowly easing the rules, first for children.
Since the lockdown ended in June, the regions have taken responsibility for managing the pandemic, with the state of emergency granting them the legal rights to enforce a curfew and other restrictions.
But it does not give them the power to impose a regional lockdown — which can only be done by the central government.
Castille and Leon, one of the worst-hit regions, has asked the government to impose a brief lockdown in the area but that request was turned down.
Neighbouring Extramadura, a landlocked region flanking Portugal which has the highest incidence in the country, has shuttered bars, restaurants and all non-essential shops for several weeks.
And the northeastern region of Catalonia on Thursday introduced new rules meaning residents cannot leave their town or city without a valid reason.
Shopping centres and gyms have been closed there, bars and restaurants can serve only breakfast or lunch, and at the weekend, only essential shops can open.