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The CDC has a webpage that lists "Table 1. Deaths involving coronavirus disease 2019 (COVID-19) and pneumonia reported to NCHS by week ending date, United States. Week ending 2/1/2020 to 4/4/2020.*" with column "All COVID-19 Deaths (U07.1)" showing 3307 deaths.

But on the CDC page "Cases in the US", it says the total deaths for just COVID-19 is 12,064.

Why does the CDC website say there are ~9,000 more deaths when not tracking pneumonia?

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    The CDC data are simply extremely incomplete, and have been for well over a month now. – Bryan Krause Apr 8 at 14:44
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Your first link says the delays are due to manual processing

Provisional counts of deaths are underestimated relative to final counts. This is due to the many steps involved in reporting death certificate data. When a death occurs, a certifier (e.g. physician, medical examiner or coroner) will complete the death certificate with the underlying cause of death and any contributing causes of death. In some cases, laboratory tests or autopsy results may be required to determine the cause of death. Completed death certificate are sent to the state vital records office and then to NCHS for cause of death coding. At NCHS, about 80% of deaths are automatically processed and coded within seconds, but 20% of deaths need to manually coded, or coded by a person. Deaths involving certain conditions such as influenza and pneumonia are more likely to require manual coding than other causes of death. Furthermore, all deaths with COVID-19 are manually coded. Death certificates are typically manually coded within 7 days of receipt, although the coding delay can grow if there is a large increase in the number of deaths. As a result, underestimation of the number of deaths may be greater for certain causes of death than others.

Your second link says it includes presumptive deaths; so not confirmed as in the first link.

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Dr. Chiu is (roughly) correct. To add a bit more detail to this: those are also two different CDC reporting mechanisms "owned" by two different parts of the CDC.

  • The one that reports Covid deaths+pneumonia (with much fewer Covid deaths) is a "traditional" channel that has been established a long time ago, called the National Vital Statistics System (NVSS); it's "onwed" by the National Center for Health Statistics (NCHS). They basically collect data on all deaths (with all causes), what you see there (on Covid+penumonia) is just an extract from a [much] bigger data set. The page starts with

    The provisional counts for coronavirus disease (COVID-19) deaths are based on a current flow of mortality data in the National Vital Statistics System. National provisional counts include deaths occurring within the 50 states and the District of Columbia that have been received and coded as of the date specified. It is important to note that it can take several weeks for death records to be submitted to National Center for Health Statistics (NCHS), processed, coded, and tabulated.

  • The other channel (which reports just [more] Covid-19 deaths) has been setup much more recently and only for the purposes of Covid-19 reporting. It also tracks every Covid case individually with a PUI (Persons Under Investigation) nCoV ID based on data reported by testers etc. For this reason, its statistics also include a live Covid case count (unlike the NVSS data, which only has deaths). Once someone tracked this way (nCoV ID) dies, their status is updated in that PUI database, according to the instructions. This PUI database/channel is also "owned" by a different part of the CDC, namely the National Center for Immunization and Respiratory Diseases (NCIRD). While it's (alas) not 100% obvious from the page where the summary (with the bigger death figure) is found what its data source is (says just "reported to the CDC") this is made clear[er] elsewhere, e.g in the COVID-19 MMWR reports; see ref 6 they cite for the data--i.e the PUI forms/database.

Obviously the two databases (PUI and NVSS) are not "in sync".

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