New York E-filing Overview

Greg Hatfield Updated by Greg Hatfield

For withholding tax returns due on or after April 30, 2015, self-filers and agents (tax professionals filing for their employer clients) must electronically file and pay withholding tax returns. Filers of paper returns may be subject to penalties and delays in processing.

The New York tax department offers three methods for electronically filing withholding tax returns. Each of the three methods is described below, along with whether it is appropriate for self-filers and/or agents, and how CFS Payroll System supports the method. We believe Method 1 will be the method of choice for most of our software users. Carefully review the methods below to determine which is appropriate for your situation. No matter which method the filer uses, they must establish an Online Services Account as soon as possible.

Method 1: Tax Department Web File – The filer uses a NY Online Services Account to make withholding payments (NYS-1) and file withholding and UI tax returns (NYS-45), including wage reports (NYS-45-ATT). This method is suitable for both self-filers and agents. Employer accounts can be linked to an agent’s account to allow easy access to the agent. Filers have immediate feedback that returns have been submitted and paid.

Self-filers must create a Business Online Services Account on

Tax professionals should create a Tax Professional Online Services Account with their EFIN number from the IRS. TheOnline Services Account can be created on the NY website, The account can be linked to their clients’ business accounts. It may take up to 45 days to get an EFIN from the IRS if you don’t already have one. You can call the NY Withholding Tax Information Center at (518) 485-6654 if you need help setting up the Online Services Account.

The Web File method involves typing most of the return data into the website forms and making the payments online via ACH debit. Employee names and social security numbers will be pre-filled from the previous quarter filing.

To aid with entering employee wages data, NY offers a Copy and Paste function. Employee wage data can be formatted in an Excel spreadsheet, copied, and then pasted into the NY website.

Another aid to entering employee wage data is Web Upload of a Wage reporting file. The wage reporting file can also be used by tax professionals to file the wage portion of Form NYS-45 for multiple clients at once. However, any feedback regarding errors in the file will be via a letter or phone call from NY days later. No immediate error reporting is available.

CFS Support – CFS Payroll System has supported New York’s Copy and Paste function since 2013. This function can be found in the Form NYS-45 module on the Online Filing Support menu. New for the 1st quarter 2015, the program can also create the Web Upload  formatted file for Wage reporting for self-filers and/or agents.

Method 2: Tax Department Web Upload – Agents can use Web Upload to file Wage reporting data, Form NYS-45, and Form NYS-1 for multiple employers at once. These are three separate Web Upload files. Although self-filers can use Web Upload to file Wage reporting data for their own company, only agents are allowed to Web Upload Forms NYS-45 and NYS-1.

Users must create an Online Services Account as described in Method 1. Once the account is setup, tax professionals must call (518) 862-3590 with NY DTF to be set up for Web Upload and indicate that they are using CFS software approved for Web Uploads. This contact number is only for Web Uploads. For assistance with Web Filing, contact the Withholding Tax Information Center at (518) 485-6654. 

Only Tax Professionals can upload Form NYS-45 and Form NYS-1 files. Both of these uploads provide immediate feedback regarding any errors.

Wage reporting files must be uploaded separately from Form NYS-45 files and can be uploaded by self-filers also. Wage reporting file uploads can be used in conjunction with manual entry of NYS-45 data as described in Method 1 above. Wage reporting file uploads do not provide immediate feedback of any errors. NY will contact the filer by phone or mail days later. Filers must file early enough to allow for timely resubmittals if necessary.

The Web Upload method is very restrictive. Tax Professionals should read and understand the restrictions before using the Web Upload method.

1. Tax Professionals must obtain an Agent number from New York when getting set up for Web Upload.

2. They must make a single Upload File for all of their clients’ NYS-45 returns for the quarter.

3. After uploading the NYS-45 file, they must print a paper voucher, NYS-45-V, from the website and make two payments, one for UI and one for withholding, in the total amount owed by all employers in the file (NYS-45), from their own bank account.

4. In order to submit a second NYS-45 file in a given quarter, agents are required to get a second Agent Number from New York.

5. Form NYS-45 must be uploaded as two separately formatted files: a Wage reporting file (Part C) and an NYS-45 file (Parts A, B, and D). The restrictions noted above pertain to the NYS-45 file, not the Wage reporting file.

6. Form NYS-1 can be uploaded multiple times during the quarter, with multiple employer returns in the file, as required by the form's variable due date. See the NYS-1 instructions. However, it still requires a single payment after each upload for the entire amount due for all employers in the file. After uploading the file, the NYS-1 can be paid using a paper voucher printed from the website (NYS-1-V) or via online ACH debit.

7. Self-filers can only upload the Wage reporting file, not the NYS-45 or NYS-1 file.

CFS Support – Beginning with the 1st quarter 2015, CFS Payroll System can make all three Web Upload files: Wage reporting file, NYS-45, and NYS-1. CFS Payroll System has successfully submitted test files for all three Web Upload files and has been approved by New York. Tax Professionals obtaining Agent Numbers must tell New York that they are using approved CFS Payroll System as their software. Although test files are not required by users of CFS Payroll System, New York encourages agents to submit test files to verify that they are properly completing the forms.

Method 3: FSET compatible softwareCurrently CFS is not able to support FSET. FSET (Federal/State Employment Taxes) is a method available to third-party transmitters to file withholding returns, wage reports, and UI information. CFS is not a third-party transmitter or payroll processor. We cannot accept our customer’s returns and file for them.

How did we do?

NYS-45/NYS-1 - E-filing (Web Upload Files)

Online State UI Filing Support