Morgan Stanley is still trying to account for all its staff
But they started looking for new offices and begun grappling with restoring computer and phone networks so that trading can resume.
But this figure is not exhaustive, as many firms contacted refused to release details.
An official with the New York Port Authority official has estimated that 20,000 could be dead.
Death toll still uncertain
There were 435 companies based in the twin towers, employing about 40,000 people.
Bond trader Cantor Fitzgerald - the largest dealer in US government bonds - appears to have suffered the heaviest losses for a single firm.
The company occupied the top floors of the North Tower, the first to be hit, and 800 of its 1,000 staff were still missing by early Thursday.
Investment and consultancy firm Marsh & McLennan has about 700 staff missing out of 1,700.
Thousands of professionals who worked in and around the World Trade Center are presumed dead, and rival banks have been co-operating to account for all their staff.
Web message boards
The internet has become a key tool for companies to stay in touch with their employees.
Corporate websites are showing telephone numbers where employees can check in with their firms to confirm that they are alright.
Detailed instructions are given which staff should report for work where, or whether they should stay at home for the time being.
Wrecked infrastructure
Wall Street firms are trying to patch up their operations - problems include wrecked offices, destroyed phone and IT networks - and there are fears that apparently undamaged buildings may not be safe.
Richard Grasso, chairman of the New York Stock Exchange is due to meet with lower Manhattan's phone company Verizon on Thursday for talks on the state the district's network.
The New York Stock Exchange remains closed and major banks have resisted pressure from the White House for an early reopening, according to a report in the Financial Times.
Mr Grasso said the NYSE would re-open "at the worst case" on Monday and was still aiming for trading to resume on Friday.
However, he stressed that nothing should get in the way of the rescue operation: "We don't want to bring hundreds of thousands of people into Manhattan that could in any way impede that recovery process."
The bond market, however, is due to reopen on Thursday at 1200 GMT, enabling trade in US government bonds.
Move to the suburbs
The destruction has wiped out 12% of lower Manhattan's office space, about 12m square metres.
Lehman's said it expects to operate from New Jersey "for the foreseeable future".
But attempts to resume business remain overshadowed by the loss of life.
"The shocking events of this week at the World Trade Center have not posed a financial problem for Morgan Stanley but a deeply human one", said the bank's chairman, Philip Purcell.
Morgan Stanley, the largest tenant in one of the two towers, said the "vast majority" of its 3,500 of retail brokers escaped safely and all its businesses are functioning.
Japanese firms Mizuho Holdings, Fuji Bank and Daichi Kangyo bank have 532 employees missing.
Keefe Bruyette Woods said 69 employees are missing and fellow investment banking house Sandler, O'Neill has 70 of 150 staff unaccounted for.
Janitors killed?
San-Francisco based ABM Industries said "it is far too early to assess the human toll".
It had 800 engineers, lighting technicians and janitors working in the World Trade Center.
Fiduciary Trust said 120 workers are missing, and Eurobrokers is looking for 80 people.
ICAP, formerly Garban-Intercapital, the world's largest inter-dealer broker, said the "vast majority" of its 675 staff escaped but a small number are still unaccounted for.